Package 'ribiosIO'

Subsetting for GctMatrix

Description

Subsetting for GctMatrix

Usage

## S3 method for class 'GctMatrix'
x[i, j, ...]

Arguments

x	A GctMatrix object
i	Index to subset rows, either integers, logical values, or characters. Other types will be converted to characters.
j	Index to subset columns.
...	Other parameters passed to matrix subsetting

Value

A GctMatrix object, subsetted according to the given indices.

Examples

m1 <- matrix(1:6, nrow=3, dimnames=list(sprintf("G%d", 1:3), sprintf("S%d", 1:2)))
gm1 <- GctMatrix(m1, desc=sprintf("Gene%d", 1:3))
gm1[1:2,]
gm1[c(TRUE, FALSE, TRUE),]
gm1[c("G3", "G1"),]
gm1[1:3,2:1]
gm1[1,]
gm1[,-1]

---

Transform a data.frame to a numeric matrix without characters coereced as factors

Description

Transform a data.frame to a numeric matrix without characters coereced as factors

Usage

as_numeric_matrix(df, warning = FALSE)

Arguments

df	A data.frame
warning	Logical, whether the function should warn when non-numeric characters are transformed

Value

A numeric matrix

---

Coerce a GctMatrix object into a matrix

Description

Coerce a GctMatrix object into a matrix

Usage

## S3 method for class 'GctMatrix'
as.matrix(x, ...)

Arguments

x	A GctMatrix object
...	Not used

Value

A matrix with a desc attribute

Examples

m1 <- matrix(1:6, nrow=3, dimnames=list(sprintf("G%d", 1:3), sprintf("S%d", 1:2)))
gm1 <- GctMatrix(m1, desc=sprintf("Gene%d", 1:3))
print(gm1)
print(as.matrix(gm1))

---

Column bind (cbind) two GctMatrix objects

Description

Column bind (cbind) two GctMatrix objects

Usage

cbindGct(
  gctMatrix1,
  gctMatrix2,
  feature = c("union", "intersection"),
  missingValue = 0
)

Arguments

gctMatrix1	The first object
gctMatrix2	The second object
feature	What happens if the set of the features in both objects differ? Either union or intersection is possible.
missingValue	Missing values, NA or numeric values (such as 0) are accepted

Value

A larger matrix, with gctMatrix1 on the left and gctMatrix2 on the right, with merged features and descriptions.

Examples

m1 <- matrix(1:6, nrow=3, dimnames=list(sprintf("G%d", 1:3), sprintf("S%d", 1:2)))
m2 <- matrix(c(9:7, 12:10), nrow=3, dimnames=list(sprintf("G%d", 3:1), sprintf("S%d", 3:4)))
gm1 <- GctMatrix(m1, desc=sprintf("Gene%d", 1:3))
gm2 <- GctMatrix(m2, desc=sprintf("Gene%d", 3:1))
gm1
gm2
gm12 <- cbindGct(gm1, gm2)
gm12
m3 <- matrix(13:18, nrow=3, dimnames=list(sprintf("G%d", 2:4), sprintf("S%d", 5:6)))
gm3 <- GctMatrix(m3, desc=sprintf("Gene%d", 2:4))
gm3
gm123Intersect <- cbindGct(gm12, gm3, feature="intersect")
print(gm123Intersect, showAll=TRUE)
gm123Union <- cbindGct(gm12, gm3, feature="union")
print(gm123Union, showAll=TRUE)
gm123UnionNA <- cbindGct(gm12, gm3, feature="union", missingValue = NA)
print(gm123UnionNA)

---

Find and read-in AmpliSeq files

Description

Find and read-in AmpliSeq files into an expression matrix

Usage

find_ampliseq(dir)

read_ampliseq(files)

find_and_read_ampliseq(dir)

Arguments

dir	The top-level directory where a AmpliSeq run is saved. An example: ‘/data64/sequencing/iontorrent_data/Auto_user_PR1-139-AmpliSeqRNA_pathway_FD14_277_360/’
files	AmpliSeq files, potentially found by find_ampliseq

Details

Directory is recursively checked for files that match the name pattern ‘*.cov.xls’ (cov means coverage). Invalid links (judged by file size) are excluded.

Only data of total read counts are read-in.

Value

find_ampliseq returns a character vector of full names of valid files.

read_ampliseq returns a numeric matrix of gene expression in counts. Row names are unique gene names.

find_and_read_ampliseq combines the two functions and returns the expression matrix as read_ampliseq does.

Author(s)

Jitao David Zhang <[email protected]>

Examples

ampdir <- system.file("extdata/ampliseq-data", package="ribiosIO")
ampfiles <- find_ampliseq(ampdir)
ampmat <- read_ampliseq(ampfiles)

ampmat.onestep <- find_and_read_ampliseq(ampdir)

---

Retrieve feature (row) descriptions from a GctMatrix S3-object

Description

Retrieve feature (row) descriptions from a GctMatrix S3-object

Usage

gctDesc(gctMatrix, index)

Arguments

gctMatrix	A GctMatrix object
index	Logical or integer index

Value

Character vector, feature descriptions

Examples

m1 <- matrix(1:6, nrow=3, dimnames=list(sprintf("G%d", 1:3), sprintf("S%d", 1:2)))
gm1 <- GctMatrix(m1, desc=sprintf("Gene%d", 1:3))
gctDesc(gm1)
gctDesc(gm1, 1:2)

---

Create a GctMatrix object

Description

Create a GctMatrix object

Usage

GctMatrix(matrix, desc)

Arguments

matrix	A numeric matrix
desc	Character vector of feature description, length must equal nrow of the matrix

Value

A GctMatrix object

Examples

m1 <- matrix(1:6, nrow=3, dimnames=list(sprintf("G%d", 1:3), sprintf("S%d", 1:2)))
m2 <- matrix(c(9:7, 12:10), nrow=3, dimnames=list(sprintf("G%d", 3:1), sprintf("S%d", 3:4)))
gm1 <- GctMatrix(m1, desc=sprintf("Gene%d", 1:3))
gm2 <- GctMatrix(m2, desc=sprintf("Gene%d", 3:1))
print(gm1)
print(gm2)

---

Convert a GctMatrix into a long data frame

Description

Convert a GctMatrix into a long data frame

Usage

gctMatrix2longdf(gctMatrix)

Arguments

gctMatrix

A GctMatrix object

Value

A data.frame with four columns: feature, desc, sample, and value

Examples

idir <- system.file("extdata", package="ribiosIO")
sample.gct.file <- file.path(idir, "test.gct")
test.mat <- read_gct_matrix(sample.gct.file, keep.desc=TRUE)
test.long <- gctMatrix2longdf(test.mat)

---

Get the data directory

Description

Get the data directory

Usage

getDataDir()

Value

A directory The value stored in options is returned

---

Get file names for data import/export

Description

Get file names for data import/export

Usage

iofile(x = NULL)

Arguments

x

File or directory name Quite often we need to import and export data (especially bulky files) into a directory other than the local file. This function is a shortcut to get full names of import/export files. The function first determines whether the option dataDir in the options of ribiosIO exists. If yes, its value will be used as the directory from/to which input/export files should be read/written. If the value does not exist yet, the function tries to use a folder named data in the current working directory as dataDir. If this local folder exists, its name will be assigned to the dataDir option. If the folder does not exist, the function will report an error and quit. The steps above guarantees that there is an option named dataDir, pointing to a directory where files are read from or written to. The parameter x can be file or directory names in the dataDir directory. In this case, iofile(x) returns their full names. When x is missing or NULL, iofile() returns the value of dataDir. A common usage for the later case is dir(iofile()).

Value

Character string, the full path to the data directory (when x is NULL) or the full file path(s) within the data directory.

Examples

setDataDir(system.file("extdata", package="ribiosIO"))
dir(iofile())
readLines(iofile("test.gct"), n=2)

---

Check if a file encodes a factor

Description

Check if a file encodes a factor

Usage

is_factor_file(con = stdin())

is_cls_file(con = stdin())

Arguments

con	Connection from which to read the file

Value

Logical, TRUE if the file is a valid CLS factor file, FALSE otherwise.

Examples

set.seed(1887)
tempfac <- factor(sample(LETTERS, 30, replace=TRUE), levels=sample(LETTERS))
tempfile <- tempfile()
write_factor(tempfac, tempfile)
is_factor_file(tempfile)
write_factor(tempfac, tempfile, sep=" ")
is_factor_file(tempfile)

---

Test a file is a GCT file or not

Description

Test a file is a GCT file or not

Usage

isGctFile(file, strict.column.names = FALSE)

Arguments

file	Character string, a file name
strict.column.names	Logical, whether the names of the first two columns must be 'NAME(tab)Description'

Details

A file is a valid GCT file if it meets following three rules:

1. The first line of the file is #1.2

2. The second line contains number of rows and number of columns, separated by a tab.

3. The rest of file contain a rectangular matrix, with the first two columns named NAME and Description respectively.

Value

A logical value: TRUE means file is of the GCT format.

References

https://software.broadinstitute.org/cancer/software/genepattern/file-formats-guide

See Also

read_gct_matrix to read in GCT files

Examples

myInFile <- system.file("extdata/test.gct", package="ribiosIO")
isGctFile(myInFile)
myInfileLS <- system.file("extdata/test_lessStrict.gct", package="ribiosIO")
isGctFile(myInfileLS)

---

Attempt to load a binary RData file

Description

The function attempts to load a binary file, returning TRUE if succeeded. Otherwise it returns FALSE.

Usage

loadFile(rDataFile, env = parent.frame())

Arguments

rDataFile	Character, RData file name
env	Environment, where should be the RData loaded into. By default it is loaded into the caller's environment.

Value

Logical, TRUE if the file was loaded successfully, FALSE otherwise.

Author(s)

Jitao David Zhang <[email protected]>

See Also

iofile can be used to find file from input data directory.

Examples

rf <- tempfile()
myData <- c(3,4,5)
save(myData, file=rf)
env <- new.env()
stopifnot(loadFile(rf, env=env))

---

Load an object by its name from a RData file

Description

Load an object by its name from a RData file

Usage

loadObject(file, obj = NULL, verbose = FALSE)

Arguments

file	A RData file
obj	Object name. If set as NULL, all objects are returned
verbose	Whether the loading process should be verbose, see load

Value

The object loaded from the RData file. If obj is NULL, returns the first object found.

---

Load objects from a RData file and return them in an environment

Description

Load objects from a RData file and return them in an environment

Usage

loadObjectInEnv(file, obj = NULL, verbose = FALSE)

Arguments

file	A RData file
obj	Character string(s), optional object names. If set as NULL, all objects are returned
verbose	Whether the loading process should be verbose, see load

Value

An environment containing the loaded objects.

---

Load an object from a RDS file and returns a logical flag

Description

Load an object from a RDS file and returns a logical flag

Usage

loadRDS(rdsFile, variableName, refhook = NULL)

Arguments

rdsFile	Character string, name of the rds file to be loaded
variableName	Character string or variable name, variable name to which the loaded value is assigned to
refhook	Logical, passed to readRDS

Value

Logical, TRUE if the file loading was successful, otherwise FALSE

---

Convert a long data.frame into a GctMatrix

Description

Convert a long data.frame into a GctMatrix

Usage

longdf2gctMatrix(
  longdf,
  row.col = 1L,
  desc.col = 2,
  column.col = 3,
  value.col = 4,
  missingValue = NULL
)

Arguments

longdf	A data.frame object
row.col	Integer or character string, index or name of the column in which row names are stored
desc.col	Integer or character string,, index or name of the column in which feature descriptions are stored
column.col	Integer or character string, index or name of the column in which sample names are stored
value.col	Integer or character string, index or name of the column in which values are stored
missingValue	Value used for missing values. If NULL, missing values are reported as NA and a warning will be raised if any value is missing. If NA, missing values are reported as NA and no warning is raised.

Value

A GctMatrix object

Examples

idir <- system.file("extdata", package="ribiosIO")
sample.gct.file <- file.path(idir, "test.gct")
test.mat <- read_gct_matrix(sample.gct.file, keep.desc=TRUE)
test.long <- gctMatrix2longdf(test.mat)
test.rmat <- longdf2gctMatrix(test.long)

---

Supress warning optionally

Description

Supress warning optionally

Usage

optional_suppress_warning(expr, suppress = TRUE)

Arguments

expr	R expression
suppress	Logical, whether or not to suppress warnings

Value

side effect is used

---

Print method for GctMatrix object

Description

Print method for GctMatrix object

Usage

## S3 method for class 'GctMatrix'
print(x, showAll = FALSE, ...)

Arguments

x	A GctMatrix object
showAll	Logical, whether all values should be printed
...	Paramters passed to the default method of print

Value

No return value, called for side effects (prints to console).

Examples

m1 <- matrix(1:6, nrow=3, dimnames=list(sprintf("G%d", 1:3), sprintf("S%d", 1:2)))
gm1 <- GctMatrix(m1, desc=sprintf("Gene%d", 1:3))
gm1
mBig <- matrix(round(rnorm(1000),3),
   nrow=100, dimnames=list(sprintf("G%d", 1:100), sprintf("S%d", 1:10)))
gmBig <- GctMatrix(mBig, desc=sprintf("Gene%d", 1:100))
gmBig
print(gmBig, showAll=TRUE)

---

Read bedcov output of AmpliSeq amplicons and convert them to read counts

Description

Read bedcov output of AmpliSeq amplicons and convert them to read counts

Usage

read_ampliseq_bedcovgct(file, bedFile)

Arguments

file	Character string, a GCT file containing bedcov output of amplicons
bedFile	Character string, an annotated BED file encoding amplicons

Value

A GctMatrix object containing read counts

The function is used to convert read base counts returned by samtools bedcov to read counts using Amplicon information encoded in the bed file

See Also

read_annotated_ampliseq_amplicons

Examples

bedlines <- paste0("#track type=bedDetail ionVersion=4.0 name=\"IAD50039-4_IAD87652-4_Design\"",
 "solution_type=4 description=\"TargetRegions_AmpliSeqID_IAD50039 AmpliSeq_Version=3.0.1",
 " Workflow=RNA merged with TargetRegions_AmpliSeqID_IAD87652 AmpliSeq_Version=4.48 Workflow=RNA\"",
 " color=77,175,74 priority=2", "\n",
 "NM_000014\t3316\t3421\tAMPL1384\t.\tGENE_ID=A2M;EntrezGeneID=2", "\n",
 "NM_005502\t2488\t2589\tAMPL28385508\t.\tGENE_ID=ABCA1;EntrezGeneID=19","\n",
 "NM_000927\t2520\t2624\tAMPL5599607\t.\tGENE_ID=ABCB1;EntrezGeneID=5243","\n",
 "NM_000443\t1367\t1470\tAMPL5513474\t.\tGENE_ID=ABCB4;EntrezGeneID=5244")
 gctLines <- paste0("#1.2", "\n",
 "3\t3","\n",
 "NAME\tDescription\tS1\tS2\tS3","\n",
 "A2M\tNM_000014\t105\t210\t315", "\n",
 "ABCA1\tNM_005502\t202\t303\t404", "\n",
 "ABCB1\tNM_000927\t312\t416\t520")
 bedcovGct <- read_ampliseq_bedcovgct(textConnection(gctLines), 
   textConnection(bedlines))
 bedcovGct

---

Read AmpliSeq amplicon informaiton from an annotated BED file

Description

Read AmpliSeq amplicon informaiton from an annotated BED file

Usage

read_annotated_ampliseq_amplicons(bedFile)

Arguments

bedFile

Character string, an annotated BED file with Gene_ID (gene symbols) and EntrezGeneID (Entrez Gene IDs) in the eighth column.

Value

A data.frame, besides reporting the columns in the BED file, contains following additional annotation information:

1. Amplicon

2. GeneID

3. GeneSymbol

4. RefSeq

5. Length

Note

There are several versions of BED file used. This function works only with the latest version.

See Also

read_bed

Examples

lines <- paste0("#track type=bedDetail ionVersion=4.0 name=\"IAD50039-4_IAD87652-4_Design\"",
 "solution_type=4 description=\"TargetRegions_AmpliSeqID_IAD50039 AmpliSeq_Version=3.0.1",
 " Workflow=RNA merged with TargetRegions_AmpliSeqID_IAD87652 AmpliSeq_Version=4.48 Workflow=RNA\"",
 " color=77,175,74 priority=2", "\n",
 "NM_000014\t3316\t3421\tAMPL1384\t.\tGENE_ID=A2M;EntrezGeneID=2", "\n",
 "NM_005502\t2488\t2589\tAMPL28385508\t.\tGENE_ID=ABCA1;EntrezGeneID=19","\n",
 "NM_000927\t2520\t2624\tAMPL5599607\t.\tGENE_ID=ABCB1;EntrezGeneID=5243","\n",
 "NM_000443\t1367\t1470\tAMPL5513474\t.\tGENE_ID=ABCB4;EntrezGeneID=5244")
 read_annotated_ampliseq_amplicons(textConnection(lines))

---

Read a BED file

Description

Read a BED file

Usage

read_bed(file, ...)

Arguments

file	Character string, name of a BED file.
...	Other parameters passed to read.table. If not specified, default settings are used.

Value

A data.frame containing all information in the BED file.

References

Definition of BED files can be found at https://www.ensembl.org/info/website/upload/bed.html.

See Also

read.table

Examples

lines <- paste0("#track type=bedDetail ionVersion=4.0 name=\"IAD50039-4_IAD87652-4_Design\"",
 "solution_type=4 description=\"TargetRegions_AmpliSeqID_IAD50039 AmpliSeq_Version=3.0.1",
 " Workflow=RNA merged with TargetRegions_AmpliSeqID_IAD87652 AmpliSeq_Version=4.48 Workflow=RNA\"",
 " color=77,175,74 priority=2", "\n",
 "NM_000014\t3316\t3421\tAMPL1384\t0\t+\t.\tGENE_ID=A2M;EntrezGeneID=2", "\n",
 "NM_005502\t2488\t2589\tAMPL28385508\t0\t+\t.\tGENE_ID=ABCA1;EntrezGeneID=19","\n",
 "NM_000927\t2520\t2624\tAMPL5599607\t0\t+\t.\tGENE_ID=ABCB1;EntrezGeneID=5243","\n",
 "NM_000443\t1367\t1470\tAMPL5513474\t0\t+\t.\tGENE_ID=ABCB4;EntrezGeneID=5244")
 read_bed(textConnection(lines))

---

qRead BioKit expression file into a data.frame

Description

qRead BioKit expression file into a data.frame

Usage

read_biokit_exprs(filename)

Arguments

filename

A BioKit expression file The function uses an efficient C routine to read BioKit expression files. An Roche NGS expression file is eseentially a tab-delimited file. THe first six columns are mandatory (feature/tag name, multiple mapping RPKM, multiple mapping read count, unique mapping RPKM, unique mapping read count, and multiple mapping proportion). Right to these columns there can be arbitrary numbers of columns appended to annotate the features. In the current output, rows may have different numbers of columns: particularly for features without corresponding items in the annotation file used in the pipeline, their rows will contain the mandatory columns plus one extra column with the value “unknown”. This is handled automatically by the function.

Value

A data.frame contains both mandatory and additional columns. The first column of the expression file will be used as the row names of the data.frame object.

See Also

read_gct for reading gct files, a commonly used file format for expression data.

Examples

biokitExampleFile <- system.file("extdata/biokit_expression_files/biokit-output-1.expression",
package="ribiosIO")
biokitExprs <- read_biokit_exprs(biokitExampleFile)

---

Read CHIP file

Description

The CHIP file format is commonly used to annotate probesets or other identifiers to gene symbols and gene names. This function imports CHIP files, using a C procedure to accelerate the speed.

Usage

read_chip(x)

Arguments

x

File name

Details

The current implementation only parses the first three columns and ignores the rest of columns. This behavior may change in future versions to provide larger flexibility of parsing CHIP-like files.

Value

A data.frame is returned with three columns: ProbeSetID, GeneSymbol and GeneTitle. The column names are concordant with the GSEA convention, except that the empty spaces are omitted.

Author(s)

Jitao David Zhang <[email protected]>

References

BROAD institute GSEA manual, available at https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats.

Examples

testFile <- system.file("extdata/test.chip", package="ribiosIO")
  testChip <- read_chip(testFile)
  head(testChip)
  stopifnot(identical(colnames(testChip), c("ProbeSetID", "GeneSymbol", "GeneTitle")))

---

Read tab-delimited result files from DAVID Bioinformatics Resources

Description

Read tab-delimited result files from DAVID Bioinformatics Resources

Usage

read_david(file)

Arguments

file	A file from DAVID Bioinformatics Resources

Value

A data.frame containing all information encoded in the file

Examples

davidFile <- system.file("extdata/example-DAVID-output-subset.txt", package="ribiosIO")
davidResult <- read_david(davidFile)

---

Read an expression matrix from file

Description

Read an expression matrix from file. The file is either a GCT format file, a tab-delimited file or a space-delimited file.

Usage

read_exprs_matrix(x)

Arguments

x

File name

Details

An expression matrix of size m x n contains exprssion levels of m features in n samples. This function supports three commonly used file formats for expression levels: GCT format, tab-delimited file and space-delimited file.

Value

A matrix

Note

The function uses a very simple logic to guess whether the file is tab-delimited or space-delimited: it reads in the first n lines (currently n=3), and checks whether there is any tab character (\t): if yes, the file is parsed as tab-delmited, otherwise as space-delimited. Therefore, a space-delimited file should not contain tabs in case it needs to be parsed.

From ribiosIO version 1.0.2, this function supports duplicated row names.

From ribiosIO version 1.0-21, this function supports matrix file in which the second column is not numeric. This can happen, for instance, if the user decides to include descriptions. If such descriptions are detected, they are stored in the attribute “desc” so as to be later written into gct files.

From ribiosIO version 1.0-39, the function tolerates non-numeric values (such as '5?') in tab-delimited files better. However note that such values in the second column will cause problem because they will make the program interpret the second column as description but not numeric values.

Author(s)

Jitao David Zhang <jitao_david.zhang at roche.com>

See Also

The function calls internally the read_gct_matrix function to parse GCT files.

Examples

testfile.path <- system.file("extdata", package="ribiosIO")

## import gct
read_exprs_matrix(file.path(testfile.path,"test_read_exprs_matrix.gct"))

## import tab-separated file
read_exprs_matrix(file.path(testfile.path, "test_read_exprs_matrix.tsv"))

## import space-separated file
read_exprs_matrix(file.path(testfile.path, "test_read_exprs_matrix.txt"))

## import tab-separated file with descriptions
read_exprs_matrix(file.path(testfile.path, "test_read_exprs_matrix_desc.tsv"))

## import tab-separated file with non-numeric values
read_exprs_matrix(file.path(testfile.path, "test_nonnumbers.txt"))

---

Read in a factor writtin in the CLS format

Description

Read in a factor writtin in the CLS format

Usage

read_factor(con = stdin(), offset = 0)

read_cls(con = stdin(), offset = 0)

Arguments

con	File or connection to read file from
offset	The integer representing the first level, default is set to 0, for some software it can be set to 1

Value

A factor with levels as defined in the CLS file.

Note

The original CLS format specifies that both tab or space can be used as separators. This makes it unable to represent factors with sapces in levels. In order to accomodate CLS format for these factors, we propose using tab as separators in CLS files when encoding factors in R. The default setting of read_factor and write_factor uses tab. Though read_factor can handle both separators, as long as in the file a separator is consistenly used.

See Also

write_factor

Examples

set.seed(1887)
tempfac <- factor(sample(LETTERS, 30, replace=TRUE), levels=sample(LETTERS))
tempfile <- tempfile()
write_factor(tempfac, tempfile)
stopifnot(identical(tempfac, read_factor(tempfile)))

write_factor(tempfac, tempfile, sep=" ")
stopifnot(identical(tempfac, read_factor(tempfile)))

idir <- system.file("extdata", package="ribiosIO")
sample.cls <- read_factor(file.path(idir, "test.cls"))
expFac <- factor(c("Case", "Control")[c(1,0,1,0,0,1,0,0,0,1,0,1,0,0,0,1,0,1,0,0,1,1,1,1,0,0)+1],
levels=c("Case", "Control"))
stopifnot(identical(sample.cls, expFac))

---

Read (write) FASTA sequences into (from) named character vectors

Description

read_fasta reads sequences in FASTA format in named character vectors. write_fasta writes sequences stored as named character vectors into FASTA file.

Usage

read_fasta(file)

write_fasta(x, file)

Arguments

file	FASTA format file
x	Named characters

Details

Names of sequences to be written do not have to begin with the greater-than sign, as they are appended by the function when writing. Similarly, the read_fasta removes the leading greater-than sign of sequence names.

Value

For read_fasta, a named character vector of FASTA sequences.

For write_fasta, the side effect is used and no value is returned.

Author(s)

Jitao David Zhang <[email protected]>

Examples

tmpfile <- tempfile()
test.seq <- c("mySeq1"="ATGCG", "mySeq2 correct"="TTGTTCGACGT")
write_fasta(test.seq, tmpfile)
read_fasta(tmpfile)

---

Calling C routine to read GCT file into a matrix

Description

The function read_gct_matrix calls the C routine read_gct to read GCT file into a matrix.

Usage

read_gct_matrix(gct.file, keep.desc = TRUE)

read_gctstr_matrix(string, keep.desc = TRUE)

Arguments

gct.file	Character, name of a gct-format file
keep.desc	Logical, whether the description of features should be returned as an attribute of the matrix
string	Character string, a character string in the GCT-file format

Details

The function read_gctstr_matrix calls the C rountine as well, to parse a character string in the GCT file format into a matrix.

This function reads GCT files into a matrix, which is a basic data structure of R. For integration with Bioconductor's ExpressionSet objects, consider using the ribiosExpression package (available on GitHub).

Value

An matrix, optionally with feature descriptions as an attribute (desc) when keep.desc is set to TRUE.

Author(s)

Jitao David Zhang <[email protected]>

See Also

isGctFile to test if a file is in GCT format.

Examples

idir <- system.file("extdata", package="ribiosIO")
sample.gct.file <- file.path(idir, "test.gct")

test.mat <- read_gct_matrix(sample.gct.file, keep.desc=TRUE)
test.simmat <- read_gct_matrix(sample.gct.file, keep.desc=FALSE)

sample.gct.string <- paste(readLines(sample.gct.file),collapse="\n")
teststr.mat <- read_gctstr_matrix(sample.gct.string, keep.desc=TRUE)

---

Read gene-sets in a GMT file into a data.frame

Description

Read gene-sets in a GMT file into a data.frame

Usage

read_gmt_dataframe(gmt.file, description = FALSE)

Arguments

gmt.file	Character, name of one gmt-format file
description	Logical, whether the result should contain descriptions of gene-sets as a column.

Value

A data.frame. If description is set to FALSE, the data.frame contains two columns: geneset and gene; otherwise, it contains three columns: geneset, description, and gene.

Examples

idir <- system.file("extdata", package="ribiosIO")
sample.gmt.file <- file.path(idir, "test.gmt")

testGmtDataframe <- read_gmt_dataframe(sample.gmt.file)

---

Calling C routine to read GMT file into a list

Description

The function read_gmt_list calls the C routine read_gmt to read GMT file into a list.

Usage

read_gmt_list(gmt.file)

Arguments

gmt.file

Character, name of one gmt-format file

Details

Empty lines or lines without genes are omitted.Empty fields in “genes” are omitted as well.

Value

A list, the length of which equals the number of genesets. Each list contains three items:

name	Character, gene set name
description	Character, gene set description
genes	Character vector, genes in the set

Author(s)

Jitao David Zhang <[email protected]>

Examples

idir <- system.file("extdata", package="ribiosIO")
sample.gmt.file <- file.path(idir, "test.gmt")

test.gmt <- read_gmt_list(sample.gmt.file)

---

Read the Data block of Illumina sample sheet as data.frame

Description

Read the Data block of Illumina sample sheet as data.frame

Usage

read_illumina_sampleSheet(file, sep = ",")

Arguments

file	An Illumina SampleSheet, with one Data block
sep	Character, separator between columns, comma by default

Value

A data.frame of the data block

Examples

myText <- paste("[Header]",
  "IEMFileVersion,5",
  "",
  "[Reads]",
  "51",
  "1",
  "[Data]",
  "Lane,Sample_ID,Description",
  "1,1,Sample1",
  "1,2,Sample2",
  "2,3,Sample3",
  "2,4,Sample4", sep="\n")
read_illumina_sampleSheet(textConnection(myText))

---

Read pheno data from CLS or tab-delimited file

Description

Read pheno (sample annotation) data from CLS file or tab-delimited file (sample information file).

Usage

read_pheno(file)

read_pheno_factor(file)

Arguments

file	A CLS file or tab-delimited file

Details

read_pheno returns a data.frame.

read_pheno_factor returns a factor, indicating sample groups. If the input file is a tab-delimited file, it filters out columns which are identical for all samples and columns which are unique for each sample. Consequently the remaining covariates are concatenated by the underscore character to form a factor. See examples below

Value

read_pheno returns a data.frame containing sample annotations. In case of CLS input file, the data.frame contains two columns: Array (indices of arrays) and Class (classes indexed in the GCT file). In case of tab-delimited file, the file will be parsed into the data.frame, assuming the file having column names but no row names.

Author(s)

Jitao David Zhang <[email protected]>

References

For CLS and sample information file formats, see the GenePattern file formats documentation at https://software.broadinstitute.org/cancer/software/genepattern/file-formats-guide.

See Also

read_cls and read.csv.

Examples

testClsFile <- system.file("extdata/test.cls", package="ribiosIO")
testPhenoFile <- system.file("extdata/testSampleInfo.txt",
package="ribiosIO")

(clsPheno <- read_pheno(testClsFile))
(txtPheno <- read_pheno(testPhenoFile))

## read_pheno_factor
(clsPhenoClass <- read_pheno_factor(testClsFile))
(txtPhenoClass <- read_pheno_factor(testPhenoFile))

testPhenoFileCov <- system.file("extdata/testSampleInfo-cov.txt",package="ribiosIO")
read_pheno_factor(testPhenoFileCov)

---

Read AmpliSeq amplicon informaiton from an raw BED file

Description

Read AmpliSeq amplicon informaiton from an raw BED file

Usage

read_raw_ampliseq_amplicons(bedFile)

Arguments

bedFile

Character string, a raw BED file coming from the AmpliSeq design pipeline (version 7.41+)

Value

A data.frame, besides reporting the columns in the BED file, contains following additional annotation information:

1. Amplicon

2. GeneSymbol (which may not be up-to-date)

3. RefSeq

4. Length

Examples

lines <- paste0("#track type=bedDetail ionVersion=4.0 name=\"IAD50039-4_IAD87652-4_Design\"",
 "solution_type=4 description=\"TargetRegions_AmpliSeqID_IAD50039 AmpliSeq_Version=3.0.1",
 " Workflow=RNA merged with TargetRegions_AmpliSeqID_IAD87652 AmpliSeq_Version=4.48 Workflow=RNA\"",
 " color=77,175,74 priority=2", "\n",
 "NM_000014\t3316\t3421\tAMPL1384\t.\tA2M", "\n",
 "NM_005502\t2488\t2589\tAMPL28385508\t.\tABCA1","\n",
 "NM_000927\t2520\t2624\tAMPL5599607\t.\tABCB1","\n",
 "NM_000443\t1367\t1470\tAMPL5513474\t.\tABCB4")
 read_raw_ampliseq_amplicons(textConnection(lines))

---

Read lines, thereby trimming empty spaces around the strings and removing empty lines

Description

Read lines, thereby trimming empty spaces around the strings and removing empty lines

Usage

read_trimmed_lines(file, skipNul = TRUE, ...)

Arguments

file	A text file
skipNul	Skip NULL line (passed to readLines)
...	Other paratmers than skipNul passed to readLines

Value

Character vector of trimmed, non-empty lines.

Examples

lines <- "  ABC \n\tHBV\n\nFCB  \n\n"
trimmedLines <- read_trimmed_lines(textConnection(lines))
stopifnot(identical(trimmedLines, c("ABC", "HBV", "FCB")))

---

Read in numeric matrix from tab-delimited format written by writeMatrix

Description

readMatrix reads a matrix written by writeMatrix into a R session

Usage

readMatrix(file, row.names = TRUE, as.matrix = TRUE, ...)

Arguments

file	file to be read in
row.names	Logical, whether the first column contains row names (should be consistent with the setting in writeMatrix)
as.matrix	Logical, whether the data.frame object should be cast into a matrix
...	Other parameters passed to read.table, for instance stringsAsFactors. Following parameters are not allowed to change: header, sep, quote, dec, check.names, strip.wrhite, comment.char.

Details

Default behaviour of read.table is adapted to the convention used in writeMatrix

Value

Matrix when as.matrix is set to TRUE and otherwise data.frame

Examples

test.mat <- matrix(rnorm(1000), nrow=10, dimnames=list(LETTERS[1:10], 1:100))
tmpfile <- tempfile()
writeMatrix(test.mat, tmpfile)
readin.mat <- readMatrix(tmpfile)
if(require(ribiosUtils)) identicalMatrix(test.mat, readin.mat)

---

Read in data.frame from tab-delimited format written by writeMatrix

Description

readTable reads a data.frame written by writeMatrix into a R session

Usage

readTable(file, row.names = TRUE, ...)

Arguments

file	file to be read in
row.names	Logical, whether the first column contains row names (should be consistent with the settign in writeMatrix)
...	Other parameters passed to read.table, for instance stringsAsFactors. Following parameters are not allowed to change: header, sep, quote, dec, check.names, strip.wrhite, comment.char.

Details

Default behaviour of read.table is adapted to the convention used in writeMatrix

Value

A data.frame object

Examples

test.df <- data.frame(Team=c("HSV", "BVB", "VFB"), Score=c(21, 19, 17))
tmpfile <- tempfile()
writeMatrix(test.df, tmpfile)
readin.df <- readTable(tmpfile)
stopifnot(identical(as.character(readin.df$Team), c("HSV", "BVB", "VFB")))
stopifnot(identical(readin.df$Score, c(21L, 19L, 17L)))

---

Set the data directory

Description

Set the data directory

Usage

setDataDir(path)

Arguments

path	Path to the data directory

Value

NULL The value is set in the options

---

Format a string list into a data.frame

Description

Format a string list into a data.frame

Usage

strList2DataFrame(strList, colnames = names(strList), index = FALSE)

Arguments

strList	A list of character strings. Other data types (e.g. factors) are converted to strings.
colnames	Column names of the resulting data.frame, by default the names of the list
index	Logical value, whether the row.names attribute of the data.frame should be integer indexes

Value

A character matrix with list elements as columns, padded with empty strings to equal length.

Examples

myList <- list("A"=LETTERS[3:5], "B"=LETTERS[4])
strList2DataFrame(myList)
strList2DataFrame(myList, colnames=c("FirstColumn", "SecondColumn"))
strList2DataFrame(myList, colnames=c("FirstColumn", "SecondColumn"), index=TRUE)

myFacList <- list("A"=gl(2,3, labels=LETTERS[1:2]), 
    "B"=gl(3,4, labels=LETTERS[1:3]))
strList2DataFrame(myFacList)

---

Write AmpliSeq amplicon informaiton into an annotated BED file

Description

Write AmpliSeq amplicon informaiton into an annotated BED file

Usage

write_annotated_ampliseq_amplicons(
  df,
  bedFile,
  version = format(Sys.time(), "%Y%m%d")
)

Arguments

df	A data.frame containing following columns (names do not matter): chrom (RefSeq IDs) chromStart (integer) chromEnd (integer) name (Amplicon IDs) score (A single value, .) ID (in the format of GENE_ID=$GENESYMBOL;EntrezGeneID=$EG_ID)
bedFile	Character string, the output file
version	Character string, a version number. By default, the current date is used.

Value

No return value, called for side effects (writes an annotated BED file).

See Also

read_annotated_ampliseq_amplicons

Examples

mydf <- data.frame(chrom=c("NM_000014", "NM_000015", "NM_000021"),
  chromStart=c(3316, 50, 1212),
  chromEnd=c(3421, 146, 1320),
  name=c("AMPL1384", "AMPL7195", "AMPL14470"),
  score=".",
  ID=c("GENE_ID=A2M;EntrezGeneID=2",
       "GENE_ID=NAT2;EntrezGeneID=10",
       "GENE_ID=PSEN1;EntrezGeneID=5663"))
myBed <- tempfile()  
write_annotated_ampliseq_amplicons(mydf, myBed)
mydfOut <- read_annotated_ampliseq_amplicons(myBed)

---

Write a factor in the CLS format

Description

Write a factor in the CLS format

Usage

write_factor(fac, con = stdout(), offset = 0, sep = c("\t", " "))

write_cls(fac, con = stdout(), offset = 0, sep = c("\t", " "))

Arguments

fac	A factor
con	Connection to write to
offset	he integer representing the first level, default is set to 0, for some software it can be set to 1
sep	Separator used in the CLS format, can be '\t' (recommended) or ' ' (not to be used when space exists in levels)

Value

No return value, called for side effects (writes to connection).

Note

The original CLS format specifies that both tab or space can be used as separators. This makes it unable to represent factors with sapces in levels. In order to accomodate CLS format for these factors, we propose using tab as separators in CLS files when encoding factors in R. The default setting of read_factor and write_factor uses tab.

See Also

read_factor

Examples

set.seed(1887)
tempfac <- factor(sample(LETTERS, 30, replace=TRUE), levels=sample(LETTERS))
tempfile <- tempfile()
write_factor(tempfac, tempfile)
readLines(tempfile)
stopifnot(identical(tempfac, read_factor(tempfile)))

---

Write matrix in GCT file format

Description

Write matrix in GCT file format

Usage

write_gct(matrix, file = stdout(), feat.name, feat.desc, na = "")

Arguments

matrix	A numeric matrix
file	Output file name. By default the file is written to standard output
feat.name	Character vector, optional. Feature names; if missing the row names are used as feature names. If given, feat.name must be of the same length as the row number of the input matrix.
feat.desc	Character vector, optional. Feature descriptions; if missing, empty strings will be used as descriptions.
na	Character string, how 'NA' values will be printed?

Details

Input matrix will be transformed into the GCT format. The transformed texts are printed on the standard output or in specified files.

If the input matrix has NULL as row names, and the feat.name option is left missing, a warning message will be print and the NAME column of the gct file will use integer indices starting from 1.

feat.desc specifies feature descriptions. Leaving is missing, or assigning it to NA or NULL will output a description column filled with empty strings.

Value

Texts printed in stdout() or in output file.

Note

From version 1.0-22, write_gct is able to handle zero-row matrix (see examples below)

Author(s)

Jitao David Zhang <[email protected]>

See Also

read_gct_matrix to read matrix from GCT files.

Examples

tmpMatrix <- matrix(rnorm(15), nrow=3L, ncol=5L,
dimnames=list(LETTERS[1:3L], letters[1:5L]))

write_gct(tmpMatrix)
write_gct(tmpMatrix, file=tempfile())

## specify feature names
write_gct(tmpMatrix, feat.name=c("F1", "F2", "F3"))
write_gct(tmpMatrix, feat.name=c("F1", "F2", "F3"), feat.desc=NULL)
write_gct(tmpMatrix, feat.name=c("F1", "F2", "F3"), feat.desc=NA)

## specify feature names and descriptions
write_gct(tmpMatrix, feat.name=c("F1", "F2", "F3"), feat.desc=
c("Feature 1", "Feature 2", "Feature 3"))

## special case: 0-row matrix
write_gct(tmpMatrix[c(FALSE,FALSE,FALSE),,drop=FALSE])

---

Write a list of gene sets into a GMT file

Description

Write gene-sets in a GMT-list form into GMT files.

Usage

write_gmt(gmt, file, description = NULL)

Arguments

gmt	A list of gene sets. It can be either (1) a list with each item is a list of three components, named ‘name’, ‘description’ and ‘genes’, or (2) a list of gene identifiers.
file	The GMT file to create
description	Description, used in case gmt is a list of gene identifiers (e.g. without description).

Details

This function can be used, for instance, to combine multiple GMT files into a new one.

Value

Invisible NULL when the file is successfully created. Otherwise an error message will be printed.

Author(s)

Jitao David Zhang <[email protected]>

Examples

idir <- system.file("extdata", package="ribiosIO")
sample.gmt.file <- file.path(idir, "test.gmt")

test.gmt <- read_gmt_list(sample.gmt.file)

outgmt.file <- paste(tempfile(), ".gmt", sep="")

write_gmt(test.gmt[1:2], file=outgmt.file)

## a list of identifiers
testList <- list(A=LETTERS[3:5], B=LETTERS[4:7], C=12:9)
write_gmt(testList, file=outgmt.file)

---

Write a list of data.frames (tables) into files

Description

Write a list of data.frames (tables) into files

Usage

write.tableList(list, file.names, ...)

Arguments

list	A list of data frames
file.names	File names. If missing, the names of the list will be used. Must be of the same length as the list
...	Other parameters that are passed to write.table

Value

No return value, called for side effects (writes files).

Author(s)

Jitao David Zhang <[email protected]>

See Also

write.table

Examples

df1 <- data.frame(name=c("A", "B", "C"), value=1:3)
df2 <- data.frame(name=c("C", "D", "E"), value=seq(9,3,-3))
dflist <- list(file1=df1, file2=df2)

tmpdir <- tempdir()
write.tableList(dflist,
  file.names=file.path(tmpdir, c("file1.txt", "file2.txt")))

---

Export matrix into a commonly used tab-delimited format inside Roche Bioinformatics

Description

writeMatrix writes a matrix into a non-quoted, tab-delimited file.

Usage

writeMatrix(x, file, row.names = TRUE)

Arguments

x	a matrix
file	file to be written to
row.names	logical, whether row.names is appended. Default: TRUE

Details

Different from the default behaviour of write.table, an empty cell is inserted as the header of row names (equivalent to setting col.names to NA

Value

No return value, called for side effects (writes to file).

See Also

readMatrix to read in matrix

Examples

test.mat <- matrix(rnorm(1000), nrow=10)
writeMatrix(test.mat, tempfile())

---

Write a list of data.frames (tables) into file with writeMatrix

Description

Write a list of data.frames (tables) into file with writeMatrix

Usage

writeMatrix.tableList(list, file.names, row.names = TRUE, ...)

Arguments

list	A list of data frames
file.names	File names. If missing, the names of the list will be used. Must be of the same length as the list
row.names	Logical, whether row.names should be in the first, unnamed column of the output files
...	Other parameters that are passed to writeMatrix

Value

Side-effects are used

Author(s)

Jitao David Zhang <[email protected]>

See Also

writeMatrix

Examples

td <- tempdir()
cwd <- getwd()
setwd(td)
df1 <- data.frame(name=c("A", "B", "C"), value=1:3)
df2 <- data.frame(name=c("C", "D", "E"), value=seq(9,3,-3))
dflist <- list(file1=df1, file2=df2)
writeMatrix.tableList(dflist) ## two files, file1 and file2, are written
dir()
writeMatrix.tableList(dflist, file.names=c("file1.txt", "file2.txt"))
dir()
setwd(cwd)

---

Write a list of strings in a tab-delimited file

Description

Write a list of strings in a tab-delimited file

Usage

writeStrList(
  list,
  file,
  names = NULL,
  type = c("column", "row"),
  index = FALSE
)

Arguments

list	A list of character strings
file	A filename
names	Names of the list; by default the names of the list
type	Should list items written in columns or rows?
index	Logical, should integer index be printed along the elements?

Value

No return value, called for side effects (writes to file).

Examples

myList <- list("A"=LETTERS[3:5], "B"=LETTERS[4])
writeStrList(myList, file=stdout())
writeStrList(myList, file=stdout(), names=c("ListA", "ListB"))
writeStrList(myList, file=stdout(), names=c("ListA", "ListB"), type="row")
writeStrList(myList, file=stdout(), names=c("ListA", "ListB"), type="row", index=TRUE)
writeStrList(myList, file=stdout(), names=c("ListA", "ListB"), type="column", index=TRUE)

---