Package 'ribiosAnnotation'

Annotate any identifiers

Description

This annotates any identifies that can be recognized by GTI.

Usage

annotateAnyIDs(ids, orthologue = FALSE, multiOrth = FALSE)

Arguments

ids	A vector of identifiers. They must be of the same type. Supported types include Entrez GeneID, GeneSymbol, Probesets, UniProt identifiers, NCBI RefSeq mRNA identifiers, and Ensembl gene identifiers (with possible version suffixes).
orthologue	Logical, is orthologous mapping needed?
multiOrth	Logical, is more than one orthologs allowed

Value

A data.frame containing annotation information. Following columns exist at least:

1. Input Input string, it will be in the first column.

2. IDType Input ID type

3. GeneID (Human) Entrez GeneID

4. GeneSymbol (Human) official gene symbol

5. GeneName (Human) gene name

6. TaxID NCBI taxonomy ID

Author(s)

Jitao David Zhang <[email protected]>

See Also

annotateGeneIDs, annotateGeneSymbols

Examples

## Not run: 
# GeneID
annotateAnyIDs(ids=c(780, 5982, 3310, NA))

# GeneSymbol
annotateAnyIDs(ids=c("DDR1", "RFC2", "HSPA6", "HSAP6"))

# Probesets
myprobes <- c("1000_at", "1004_at", "1002_f_at", "nonsense_at")
annotateAnyIDs(myprobes)

# UniProt
annotateAnyIDs(ids=c("P38398", "Q8NDF8"))

# EnsEMBL
ensemblIDs <- c("ENSG00000197535", "ENST00000399231.7", "ENSP00000418960.2")
annotateAnyIDs(ensemblIDs)

# RefSeq
annotateAnyIDs(c("NM_000235", "NM_000498"))

## End(Not run)

---

Annotate Enesembl GeneIDs

Description

Annotate Enesembl GeneIDs

Usage

annotateEnsemblGeneIDs(ids, orthologue = FALSE, multiOrth = FALSE)

Arguments

ids	A vector of EnsemblGeneIDs in form of ENS(species)(object type)(identifier).(version). The version is optional.
orthologue	Logical, whether human orthologues should be returned. Default: FALSE
multiOrth	Logical, whether mutliple orthologues should be returned if exist. Deafult: FALSE

Value

A data.frame object containing the annotations: * GeneID EntrezGeneID * GeneSymbol Official gene symbol * Description Gene description * TaxID Taxonomy ID * Type Gene type

If orthologue is TRUE, following columns are appended: * HumanGeneID * HumanGeneSymbol * HumanDescription * HumanType

See Also

annotateEnsemblGeneIDsWithoutHumanOrtholog and annotateEnsemblGeneIDsWithHumanOrtholog

Examples

## Not run: 
  annotateEnsemblGeneIDs(ids=c("ENSG00000236453", "ENSG00000170782",
                               "ENSG00000187867"))
  annotateEnsemblGeneIDs(ids=c("ENSG00000236453", "ENSG00000170782",
                               "ENSG00000187867", NA), orthologue=TRUE)
  annotateEnsemblGeneIDs(ids=c("ENSG00000174827", "ENSMUSG00000038298",
                               "ENSG00000198483", "ENSMUSG00000038354",
                               "ENSRNOG00000054947", "ENSG00000278099"),
                        orthologue=TRUE)

## End(Not run)

---

Annotate EnsEMBL GeneID with data from EnsEMBL

Description

Annotate EnsEMBL GeneID with data from EnsEMBL

Usage

annotateEnsemblGeneIDsWithEnsembl(ids)

Arguments

ids	Character strings, Ensembl GeneIDs in form of ENS(species)(object type)(identifier).(version). The version is optional.

Details

The ensembl_genes collection is used. Note that Ensembl IDs often refer to novel transcripts which do not have identifiers in other databases like NCBI Genes. If an EnsemblID is invalid or obsolete, the fields GeneName and TaxID will be NA.

Value

A data.frame containing following columns:

• EnsemblID: The input EnsemblID

• GeneID: NCBI GeneID

• GeneSymbol: Official gene symbol

• Description: Gene description

• TaxID: Taxonomy ID

This function uses data from EnsEMBL to annotate EnsEMBL GeneIDs. For most users, it is recommended to use annotateEnsemblGeneIDs, because it uses both data from EnsEMBL and data from NCBI to perform the task.

See Also

Function annotateEnsemblGeneIDsWithNCBI annotates EnsEMBL GeneIDs with data from NCBI, and annotateEnsemblGeneIDs annotates EnsEMBL GeneIDs with both data from EnsEMBL and data from NCBI.

Examples

## Not run: 
ensIDs <- readLines(system.file(file.path("extdata/ribios_annotate_testdata",
                    "ensemble_geneids.txt"), package="ribiosAnnotation"))
ensAnno <- annotateEnsemblGeneIDsWithEnsembl(ensIDs)

## End(Not run)

---

Annotate Ensembl GeneIDs while appending human orthologs

Description

Annotate Ensembl GeneIDs while appending human orthologs

Usage

annotateEnsemblGeneIDsWithHumanOrtholog(ids, multiOrth = FALSE)

Arguments

ids	A vector of character strings, Ensembl GeneIDs in form of ENS(species)(object type)(identifier).(version). The version is optional.
multiOrth	Logical, whether mutliple orthologues should be returned if exist. Deafult: FALSE

Value

A data.frame containing following columns:

• EnsemblID: The input EnsemblID

• GeneID: NCBI GeneID

• GeneSymbol: Official gene symbol

• Description: Gene description

• TaxID: Taxonomy ID

• Type: Gene type

• HumanGeneID: NCBI GeneID of the human orthologue

• HumanGeneSymbol: Official gene symbol of the human orthologue

• HumanDescription: Gene description of the human orthologue

• HumanType: Gene type of the human orthologue

Note

Currently the human orthologs are looked up in NCBI. It remains to be changed to EnsEMBL

Examples

## Not run: 
ensIDs <- readLines(system.file(file.path("extdata/ribios_annotate_testdata",
                    "ensemble_geneids.txt"), package="ribiosAnnotation"))
enAnnoHumanOrt <- annotateEnsemblGeneIDsWithHumanOrtholog(ensIDs)

## End(Not run)

---

Annotate EnsEMBL GeneID with data from NCBI

Description

Annotate EnsEMBL GeneID with data from NCBI

Usage

annotateEnsemblGeneIDsWithNCBI(ids)

Arguments

ids	Character strings, Ensembl GeneIDs in form of ENS(species)(object type)(identifier).(version). The version is optional.

Details

The ncbi_gene2ensembl collection is used.

Value

A data.frame containing following columns:

• EnsemblID: The input EnsemblID

• GeneID: NCBI GeneID

• GeneSymbol: Official gene symbol

• Description: Gene description

• TaxID: Taxonomy ID

• Type: Gene type

This function uses data from NCBI to annotate EnsEMBL GeneIDs. For most users, it is recommended to use annotateEnsemblGeneIDs, because it uses both data from EnsEMBL and data from NCBI to perform the task.

See Also

Function annotateEnsemblGeneIDsWithEnsembl annotates EnsEMBL GeneIDs with data from Ensembl, and annotateEnsemblGeneIDs annotates EnsEMBL GeneIDs with both data from EnsEMBL and data from NCBI.

Examples

## Not run: 
ensIDs <- readLines(system.file(file.path("extdata/ribios_annotate_testdata",
                    "ensemble_geneids.txt"), package="ribiosAnnotation"))
ncbiAnno <- annotateEnsemblGeneIDsWithNCBI(ensIDs)

## End(Not run)

---

Annotate Ensembl GeneIDs with data from both EnsEMBL and NCBI

Description

Annotate Ensembl GeneIDs with data from both EnsEMBL and NCBI

Usage

annotateEnsemblGeneIDsWithoutHumanOrtholog(ids)

Arguments

ids	A vector of character strings, Ensembl GeneIDs in form of ENS(species)(object type)(identifier).(version). The version is optional.

Details

First, both EnsEMBL and NCBI annotation is queried. Next, we use the NCBI annotation as the template. Finally, we take the EnsEMBL annotation for those genes that are annotated by EnsEMBL but not by NCBI, merging the information from both sources.

Value

A data.frame containing following columns:

• EnsemblID: The input EnsemblID

• GeneID: NCBI GeneID

• GeneSymbol: Official gene symbol

• Description: Gene description

• TaxID: Taxonomy ID

• Type: Gene type

Examples

## Not run: 
ensIDs <- readLines(system.file(file.path("extdata/ribios_annotate_testdata",
                    "ensemble_geneids.txt"), package="ribiosAnnotation"))
enAnno <- annotateEnsemblGeneIDsWithoutHumanOrtholog(ensIDs)

## End(Not run)

---

Annotate Entrez GeneIDs

Description

Annotate Entrez GeneIDs

Usage

annotateGeneIDs(ids, orthologue = FALSE, multiOrth = FALSE)

Arguments

ids	A vector of integers or characters, encoding NCBI Entrez GeneIDs. It can contain NA or NULL.
orthologue	Logical, whether human orthologues should be returned. Default: FALSE
multiOrth	Logical, whether mutliple orthologues should be returned if exist. Deafult: FALSE

Value

A data.frame object containing the annotations: * GeneID EntrezGeneID * GeneSymbol Official gene symbol * Description Gene description * TaxID Taxonomy ID * Type Gene type

If orthologue is TRUE, following columns are appended: * HumanGeneID * HumanGeneSymbol * HumanDescription * HumanType

See Also

annotateGeneIDsWithoutHumanOrtholog and annotateGeneIDsWithHumanOrtholog

Examples

## Not run: 
  annotateGeneIDs(ids=c(780, 5982, 3310))
  annotateGeneIDs(ids=c(780, 5982, 3310, NA), orthologue=TRUE)
  annotateGeneIDs(ids=c(780, 1506, 1418,
                        114483548, 57300, 
                        20, 1506, 102129055),
                        orthologue=TRUE)

## End(Not run)

---

Annotate Entrez GeneIDs with the query of human orthologs

Description

Annotate Entrez GeneIDs with the query of human orthologs

Usage

annotateGeneIDsWithHumanOrtholog(ids, multiOrth = FALSE)

Arguments

ids	Vector of integer or character strings, EntrezIDs to be annotated
multiOrth	Logical, whether mutliple orthologues should be returned if exist. Deafult: FALSE

Value

A data.frame object containing the annotations: * GeneID EntrezGeneID * GeneSymbol Official gene symbol * Description Gene description * TaxID Taxonomy ID * Type Gene type * HumanGeneID * HumanGeneSymbol * HumanDescription * HumanType

Examples

## Not run: 
  annotateGeneIDsWithHumanOrtholog(ids=c(780, 5982, 3310))
  annotateGeneIDsWithHumanOrtholog(ids=c(780, 5982, 3310, NA))
  annotateGeneIDsWithHumanOrtholog(ids=c(780, 5982, 3310, NULL))
  annotateGeneIDsWithHumanOrtholog(ids=c(780, 5982, 3310, "1418"))
  annotateGeneIDsWithHumanOrtholog(ids=c(780, 5982, 3310, "NotValidGeneID"))
  annotateGeneIDsWithHumanOrtholog(ids=c(780, 5982, 3310, 1418, 5982))
  annotateGeneIDsWithHumanOrtholog(ids=c(780, 5982, 1418, 5982, 25120,
                        114483548, 57300, 20, 1506,
                        1545, 102129055))

## End(Not run)

---

Annotate Entrez GeneIDs without querying human orthologs

Description

Annotate Entrez GeneIDs without querying human orthologs

Usage

annotateGeneIDsWithoutHumanOrtholog(ids)

Arguments

ids	A vector of integers or characters, encoding NCBI Entrez GeneIDs. It can contain NA or NULL.

Details

The collection ncbi_gene_info is used.

Value

A data.frame object containing the annotations: * GeneID EntrezGeneID * GeneSymbol Official gene symbol * Description Gene description * TaxID Taxonomy ID * Type Gene type

Note

annotatemRNAs is an alias of annotateRefSeqs

Author(s)

Jitao David Zhang <[email protected]>

Examples

## Not run: 
  annotateGeneIDsWithoutHumanOrtholog(ids=c(780, 5982, 3310))
  annotateGeneIDsWithoutHumanOrtholog(ids=c(780, 5982, 3310, NA))
  annotateGeneIDsWithoutHumanOrtholog(ids=c(780, 5982, 3310, NULL))
  annotateGeneIDsWithoutHumanOrtholog(ids=c(780, 5982, 3310, "1418"))
  annotateGeneIDsWithoutHumanOrtholog(ids=c(780, 5982, 3310, "NotValidGeneID"))
  annotateGeneIDsWithoutHumanOrtholog(ids=c(780, 5982, 3310, 1418, 5982))
  annotateGeneIDsWithoutHumanOrtholog(ids=c(780, 5982, 1418, 5982, 25120,
                        114483548, 57300, 20, 1506,
                        1545, 102129055))

## End(Not run)

---

Annotate GeneSymbols

Description

Annotate GeneSymbols

Usage

annotateGeneSymbols(ids, taxId = 9606, orthologue = FALSE, multiOrth = FALSE)

Arguments

ids	Character strings, gene symbols
taxId	Integer, NCBI taxonomy ID. Default value: 9606 (human). See commonSpecies for tax id of common species.
orthologue	Logical, whether orthologues are to be returned
multiOrth	Logical, only valid when orthologue is set to TRUE, whether multiple orthologues are returned

Value

A data.frame containing following columns

GeneID

Entrez Gene ID

GeneSymbol

Official gene symbols

Description

Description

TaxID

NCBI Taxonomy ID

Type

Gene type

If orthologue is TRUE, then additional columns are appended:

HumanGeneID

Human orthologue Entrez GeneID

HumanGeneSymbol

Human orthologue official gene symbol

HumanDescription

Human orthologue gene description

HumanType

Human orthologue gene type

See Also

The function is a convenient wrapper of two functions: annotateGeneSymbolsWithoutHumanOrtholog and annotateGeneSymbolsWithHumanOrtholog.

Examples

## Not run: 
    annotateGeneSymbols(c("AKT1", "ERBB2", "NoSuchAGene", "TGFBR1"), 9606)
    annotateGeneSymbols(c("Akt1", "Erbb2", "NoSuchAGene", "Tlr7"), 
                        taxId=10116, orthologue=FALSE)
    annotateGeneSymbols(c("Akt1", "Erbb2", "NoSuchAGene", "Tlr7"), 
                        taxId=10116, orthologue=TRUE)
    annotateGeneSymbols(c("Akt1", "Erbb2", "NoSuchAGene", "Tlr7"), 
                        taxId=10116, orthologue=TRUE, multiOrth=TRUE)

## End(Not run)

---

Annotate GeneSymbol with human ortholog

Description

Annotate GeneSymbol with human ortholog

Usage

annotateGeneSymbolsWithHumanOrtholog(ids, taxId, multiOrth = FALSE)

Arguments

ids	Character strings, gene symbols
taxId	Integer, NCBI taxonomy ID. Default value: 9606 (human). See commonSpecies for tax id of common species.
multiOrth	Logical, only valid when orthologue is set to TRUE, whether multiple orthologues are returned

Value

A data.frame containing following columns:

GeneID

Entrez Gene ID

GeneSymbol

Official gene symbols

Description

Description

TaxID

NCBI Taxonomy ID

Type

Gene type

HumanGeneID

Human orthologue Entrez GeneID

HumanGeneSymbol

Human orthologue official gene symbol

HumanDescription

Human orthologue gene description

HumanType

Human orthologue gene type

Examples

## Not run: 
    annotateGeneSymbolsWithHumanOrtholog(c("Akt1", "Erbb2",
                                         "NoSuchAGene", "Tgfbr1"), 
                                         taxId=10090, multiOrth=FALSE)

## End(Not run)

---

Annotate gene symbols without human ortholog

Description

Annotate gene symbols without human ortholog

Usage

annotateGeneSymbolsWithoutHumanOrtholog(ids, taxId = 9606)

Arguments

ids	Character vector, gene symbols to be queried
taxId	Integer, NCBI taxonomy ID of the species. Default value: 9606 (human). See commonSpecies for tax id of common species.

Value

A data.frame of following columns

GeneID

Entrez Gene ID

GeneSymbol

Official gene symbols

Description

Description

TaxID

NCBI Taxonomy ID

Type

Gene type

Examples

## Not run: 
    annotateGeneSymbolsWithoutHumanOrtholog(c("AKT1", "ERBB2", 
                                            "NoSuchAGene", "TGFBR1"), 9606)
    annotateGeneSymbolsWithoutHumanOrtholog(c("Akt1", "Erbb2", 
                                            "NoSuchAGene", "Tgfbr1"), 10090)

## End(Not run)

---

Annotate human orthologs with data from NCBI

Description

Annotate human orthologs with data from NCBI

Usage

annotateHumanOrthologsWithNCBI(geneids, multiOrth = FALSE)

Arguments

geneids	Integer GeneIDs, can contain human GeneIDs.
multiOrth	Logical, whether one gene is allowed to map to multiple human orthologs? Default value is FALSE, i.e. only the first human ortholog (random choice) is returned.

Details

ncbi_gene_info and ncbi_gene_orthologs collections are used.

Value

A data.frame containing following columns: * GeneID: Input GeneID * TaxID: Taxonomy ID of the input gene * HumanGeneID: Human Entrez GeneID

This function annotates human orthologs for any GeneID, including human genes, in which case the ortholog will be itself. Use annotateNonHumanGenesHumanOrthologsWithNCBI if you are sure that input GeneIDs do not come from human.

See Also

annotateNonHumanGenesHumanOrthologsWithNCBI

Examples

## Not run: 
annotateHumanOrthologsWithNCBI(c(25120, 114483548, 57300, 20))
annotateHumanOrthologsWithNCBI(c(25120, 114483548, 57300, 20, 1506, 1545,
                                 102129055))

## End(Not run)

---

Annotate human orthologs with data from NCBI

Description

Annotate human orthologs with data from NCBI

Usage

annotateNonHumanGenesHumanOrthologsWithNCBI(geneids, multiOrth = FALSE)

Arguments

geneids	Integer GeneIDs, can contain human GeneIDs.
multiOrth	Logical, whether one gene is allowed to map to multiple human orthologs? Default value is FALSE, i.e. only the first human ortholog (random choice) is returned.

Details

ncbi_gene_info and ncbi_gene_orthologs collections are used.

Value

A data.frame containing following columns: * GeneID: Input GeneID * TaxID: Taxonomy ID of the input gene * HumanGeneID: Human Entrez GeneID

This function annotates human orthologs for any non-human genes. Use annotateHumanOrthologsWithNCBI if you are not sure whether all input GeneIDs are non-human.

See Also

annotateHumanOrthologsWithNCBI

Examples

## Not run: 
annotateNonHumanGenesHumanOrthologsWithNCBI(c(25120, 114483548, 57300, 20))
annotateNonHumanGenesHumanOrthologsWithNCBI(c(25120, 114483548, 57300, 
                                              20, 1506, 1545, 102129055))

## End(Not run)

---

Annotate protein groups for proteomics studies

Description

Annotate protein groups for proteomics studies

Usage

annotateProteinGroups(
  ids,
  delimiter = ";",
  orthologue = FALSE,
  multiOrth = FALSE
)

Arguments

ids	Character, Protein groups with identifiers (e.g. UniProt/SwissProt IDs) by the delimiter
delimiter	Character, delimiter, default semicolon
orthologue	Logical, whether human orthologues should be queried.
multiOrth	Logical, in case of multiple orthologues, whether all of them should be returned The function queries proteins in protein groups, and annotate all proteins that cannot be annotated. For protein groups in which no protein can be annotated, all proteins will be returned as they are, without annotation

Value

A data.frame with following columns: * ProteinGroup * Protein * GeneID * GeneSymbol * GeneName * TaxID In case orthologue is TRUE, human orthologue information is returned as well.

Examples

## Not run: 
annotateProteinGroups(c("A0A024RBG1;Q9NZJ9", "A0A0B4J2D5;P0DPI2",
                           "A0A0B4J2F0;A0A0U1RRL7"))

## End(Not run)

---

Annotations of all genes associated with the given TaxID

Description

The function returns annotations (see details below) of all features (probably probesets) associated with the given taxon.

Usage

annotateTaxID(taxId, orthologue = FALSE, multiOrth = FALSE)

Arguments

taxId	Integer, the TaxID of the species in interest. For instance ‘9606’ for Homo sapiens.
orthologue	Logical, whether human orthologues should be returned
multiOrth	Logical, in case orthologue is set to TRUE, whether to return multiple orthologues for one gene. Default: FALSE

Details

The function reads from the backend, the MongoDB bioinfo database.

Value

A data.frame object with very similar structure as the EG_GENE_INFO table in the database. In case orthologue is TRUE, additional columns containing human orthologue information are returned.

Rownames of the data.frame are set to NULL.

Author(s)

Jitao David Zhang <[email protected]>

Examples

## Not run: 
hsAnno <- annotateTaxID("9606")
dim(hsAnno)
head(hsAnno)

hsMtAnno <- annotateTaxID("10092")
dim(hsMtAnno)
head(hsMtAnno)

mtOrthAnno <- annotateTaxID(10090, orthologue=TRUE)
dim(mtOrthAnno)
head(mtOrthAnno)

pigMultiOrthAnno <- annotateTaxID(9823, orthologue=TRUE, multiOrth=TRUE)
dim(pigMultiOrthAnno)
head(pigMultiOrthAnno)

## End(Not run)

---

Annotate UniProt accessions or names

Description

Annotate UniProt accessions or names

Usage

annotateUniprotAccession(accessions, orthologue = FALSE, multiOrth = FALSE)

Arguments

accessions	Character strings, UniProt accessions or names
orthologue	Logical, whether orthologues are returned
multiOrth	Logical, only valid if orthologue is TRUE, whether multiple orthologues are returned instead of only one.

Examples

## Not run: 
annotateUniprotAccession(c("B4E0K5"))

## End(Not run)

---

Append human orthologs to an existing annotation dataframe

Description

Append human orthologs to an existing annotation dataframe

Usage

appendHumanOrthologsWithNCBI(anno, multiOrth = FALSE)

Arguments

anno	A data.frame containing at least two columns GeneID and TaxID. The column GeneID stores Entrez GeneIDs, which are integers (NA values and characters are tolerated). The column TaxID stores taxonomy ID, which are integers, too (again, NA values and characters are tolerated).
multiOrth	Logical, whether one row is allowed to map to multiple orthologues The function appends human orthologs to an existing annotation data.frame. It is usually called by another function. Please make sure of what you are doing if you call it directly.

Value

A data.frame with annotation and human orthologs appended.

Note

The function does not sort the rows by GeneID. It is the responsibility of the calling function to do so.

Examples

## Not run: 
anno <- data.frame(GeneID=c(780, 1506, 114483548, 102129055, NA),
                   TaxID=c(9606, 9606, 10116, 9541, NA))
appendHumanOrthologsWithNCBI(anno)

tol_anno <- data.frame(GeneID=c(780, 1506, 114483548, 102129055, NA, "NotV"),
                   TaxID=c(9606, 9606, 10116, 9541, NA, NA))
appendHumanOrthologsWithNCBI(tol_anno)

## End(Not run)

---

check single integer Tax ID

Description

check single integer Tax ID

Usage

checkSingleIntegerTaxId(taxId)

Arguments

taxId

Integer tax identifier, or character that can be converted to an integer

Value

An integer tax ID if successful, otherwise the function stops and prints error

---

Common species taxonomy IDs

Description

Common species taxonomy IDs

Usage

commonSpecies

Format

A data.frame containing three columns:

TaxID

NCBI taxonomy ID

ScientificName

Scientific name

CommonName

Common name

---

Connect to a MongoDB instance

Description

Connect to a MongoDB instance

Usage

connectMongoDB(
  instance = "bioinfo_read",
  collection = "ncbi_gene_info",
  verbose = FALSE
)

Arguments

instance	Character string, the MongoDB instance to connect to
collection	Character string, the collection to be used
verbose	Logical

Value

A pointer to a collection on the server, as returned by mongo.

See Also

loadMongodbSecrets

Examples

## Not run: 
giCon <- connectMongoDB(instance="bioinfo_read",
                        collection="ncbi_gene_info")

## End(Not run)

---

Formatting a vector for SQL SELECT query with IN syntax

Description

Prepare a vector for SQL SELECT query with the IN syntax

Usage

formatIn(x)

Arguments

x	A vector to be queried with the IN syntax

Value

A character string to be used after IN. See examples.

Author(s)

Jitao David Zhang <[email protected]>

Examples

myvec <- c("HH", "HM", "TH")
formatIn(myvec)
mysel <- "SELECT * FROM table WHERE city IN"
paste(mysel,formatIn(myvec))

---

Get all taxonomy ID and scientific names offered by NCBI

Description

Get all taxonomy ID and scientific names offered by NCBI

Usage

getAllTaxIDs()

Value

A data.frame containing two columns, TaxID and ScientificName.

Examples

## Not run: 
    all_tax_ids <- getAllTaxIDs()

## End(Not run)

---

Translate chiptypes between GTI Bioconductor naming conventions

Description

gti2bioc converts chip types from GTI array names into Bioconductor names, and bioc2gti converts Bioconductor array names to GTI names. If the array name is not valid or not found, NA will be returned.

Usage

gti2bioc(chipname)

Arguments

chipname

Character vector, chip names (types). If missing, chip types supported by both GTI and Bioconductor will be printed, see details.

Details

The translation table gtibioc was compiled manually in December 2011.

When the parameter ‘chipname’ is missing, chip types supported by both GTI and Bioconductor will be printed: gti2bioc returns a character vector of the Bioconductor names, and bioc2gti returns such a vector of the GTI names. Both vectors have the chip types in the other system as names. See examples.

Value

Chracter vector of the same length as the input

Author(s)

Jitao David Zhang <[email protected]>

Examples

bioc2gti("hgu133plus2")
bioc2gti(c("hgu133plus2", "hgu95av2", "bad_array"))
gti2bioc("HG_U95AV2")
gti2bioc(c("HG_U95AV2", "CANINE", "HG_U95A"))

## supporting empty option
bioc2gti()
gti2bioc()

---

Translation table between GTI and Bioconductor chip type names

Description

A data frame mapping GTI array names to Bioconductor array names.

Usage

gtibioc

Format

A data frame with columns:

GTI

GTI chip type name

Bioconductor

Bioconductor chip type name

Source

Compiled manually in December 2011.

---

Guess feature ID type by majority voting and annotate them

Description

Guess feature ID type by majority voting and annotate them

Usage

guessAndAnnotate(
  featureIDs,
  majority = 0.5,
  orthologue = FALSE,
  multiOrth = FALSE,
  taxId = 9606
)

Arguments

featureIDs	A vector of character strings. Other input types will be converted to character strings.
majority	Numeric value between 0 and 1. If the proportion of valid feature IDs in the input matching the pattern of a certain feature type exceeds this value, the function returns a character string representing the feature ID type.
orthologue	Logical, whether orthologue should be returned if the input features are not of human
multiOrth	Logical, in case multiple human orthologues are available, should they all be returned?
taxId	Integer, in case the input identifiers are gene symbols, the user can specify the organism to be used with the NCBI taxonomy ID. The option is passed to annotateGeneSymbols. Check out commonSpecies for matches between taxonomy ID and species names.

Value

A data.frame, containing annotations of following ID types

• GeneID

• GeneSymbol

• RefSeq

• EnsemblGeneID

• Ensembl

• UniProt

• Unknown

. In case of Unknown, a data.frame with one column (FeatureName), containing input ids, is returned.

The difference between guessAndAnnotate and annotateAnyIDs is that the later does not assume that all IDs are of the same type.

See Also

annotateAnyIDs

Examples

## Not run: 
  guessAndAnnotate(c("AKT1", "AKT2", "MAPK14"))
  guessAndAnnotate(c(1,2,14,149))
  guessAndAnnotate(c("NM_000259", "NM_000331"))
  guessAndAnnotate(c("ENST00000613858.4", "ENST00000553916.5",
       "ENST00000399229.6"))
  guessAndAnnotate(c("O60583", "P05997", "Q7Z624"))
  guessAndAnnotate(c("CM000677.2", "AB003434.2"))

## End(Not run)

---

Guess feature ID type by majority voting

Description

Guess feature ID type by majority voting

Usage

guessFeatureType(featureIDs, majority = 0.5)

Arguments

featureIDs	A vector of character strings. Other input types will be converted to character strings.
majority	Numeric value between 0 and 1. If the proportion of valid feature IDs in the input matching the pattern of a certain feature type exceeds this value, the function returns a character string representing the feature ID type.

Value

A character string, one of the following values:

• GeneID

• GeneSymbol

• RefSeq

• EnsemblGeneID

• Ensembl

• UniProt

• Unknown

. The majority voting is done in the same order

Examples

guessFeatureType(c("AKT1", "AKT2", "MAPK14"))
guessFeatureType(c(1,2,14,149))
guessFeatureType(c("NM_000259", "NM_000331"))
guessFeatureType(c("ENST00000613858.4", "ENST00000553916.5",
    "ENST00000399229.6"))
guessFeatureType(c("A2BC19", "P12345", "A0A023GPI8"))
guessFeatureType(c("CM000677.2"))

---

Retrieve human orthologs of genes of another species with its Taxonomy ID

Description

Retrieve human orthologs of genes of another species with its Taxonomy ID

Usage

humanOrthologsByTaxID(taxid)

Arguments

taxid

An integer, a NCBI taxonomy ID to identify a species, for instance 10116 for rat, 10090 for mouse, and 9541 for cyno (crab-eating macaque).

Value

A data.frame contains following columns:

GeneID

NCBI Gene ID of the query species

GeneSymbol

NCBI Gene symbol of the query species

Description

Gene description of the query species

HumanGeneID

NCBI Gene ID of the human homolog

HumanGeneSymbol

NCBI Gene symbol of the human homolog

HumanDescription

Gene description of the human homolog

Note

To query NCBI taxonomy IDs from free-text search, visit [NCBI Taxonomy Browser](https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi).

Examples

## Not run: 
## human orthologs of rat genes
ratOrths <- humanOrthologsByTaxID(10116)
## human orthologs of mouse genes
mouseOrths <- humanOrthologsByTaxID(10090)
## human orthologs of cyno genes (crab-eating macaque, Macaca fascicularis)
cynoOrths <- humanOrthologsByTaxID(9541)

## End(Not run)

---

Whether input character strings are valid feature IDs

Description

Whether input character strings are valid feature IDs

Usage

isValidFeatureID(featureIDs)

Arguments

featureIDs

A vector of character strings

Value

Logical vector of the same lenght as the input

Invalid feature IDs include NA, "-", and empty string. Other features are deedm as valid.

See Also

validFeatureIDs

Examples

featureIDs <- c("AMPK", "", "ACTB", "-")
isValidFeatureID(featureIDs)

---

Whether input strings look like Entrez GeneIDs

Description

Whether input strings look like Entrez GeneIDs

Usage

likeGeneID(featureIDs)

likeRefSeq(featureIDs)

likeEnsembl(featureIDs)

likeEnsemblGeneID(featureIDs)

likeUniProt(featureIDs)

likeGeneSymbol(featureIDs)

likeHumanGeneSymbol(featureIDs)

Arguments

featureIDs

Character strings. Input of other types are converted to them.

Value

A logical vector of the same length as input

Functions

• likeRefSeq(): tests whether input strings look like NCBI RefSeq IDs

• likeEnsembl(): tests whether input strings look like Ensembl IDs

• likeEnsemblGeneID(): tests whether input strings look like EnsemblGeneIDs

• likeUniProt(): tests whether input strings look like UniProt IDs

• likeGeneSymbol(): tests whether input strings look like gene symbols

• likeHumanGeneSymbol(): tests whether input strings look like human gene symbols

References

Regular expression of UniProt accesion numbers is available at https://www.uniprot.org/help/accession_numbers. We requirea a whole-string match additionally

The HGNC guideline is available at https://www.genenames.org/about/guidelines/

Examples

feats <- c("1234", "LOX", "345", "-", "", "NKX-1", "CXorf21", "Snail",
   "A2BC19", "P12345", "A0A023GPI8",
   "NM_000259", "NM_000259.3", "ENSG00000197535", "ENST00000399231.7")
likeGeneID(feats) 
likeGeneSymbol(feats)
likeRefSeq(feats)
likeEnsembl(feats)
likeUniProt(feats)
likeHumanGeneSymbol(feats)

---

Get secrets for MongoDB connections

Description

Get secrets for MongoDB connections

Usage

loadMongodbSecrets(file = locateSecretsFile(), instance = "bioinfo_read")

Arguments

file	The secret JSON file.
instance	String, which must be found under the mongodb section of the JSON file

Value

A list of the following items:

hostname

Hostname of the MongoDB

port

Port of the MongoDB

dbname

Database of the MongoDB

username

User name

password

Password

Examples

loadMongodbSecrets(instance="bioinfo_read")
## Not run: 
    loadMongodbSecrets(instance="decoy")

## End(Not run)

---

Guess the majority members of a character string look like human gene symbols

Description

Guess the majority members of a character string look like human gene symbols

Usage

majorityLikeHumanGeneSymbol(x, majority = 0.8)

Arguments

x	A vector of character strings
majority	A numeric value between 0 and 1, the threshold of majority voting

Value

A logical value TRUE is only returned if at least a proportion of majority members look like human gene symbols

Examples

majorityLikeHumanGeneSymbol(c("AKT1", "AKT2", "MYOA")) # TRUE
majorityLikeHumanGeneSymbol(c("Akt1", "Akt2", "Myoa")) # FALSE
majorityLikeHumanGeneSymbol(c("AKT1", "Akt2", "MYOA"), majority=0.5) # TRUE

---

Remove version suffix from Ensembl IDs

Description

Remove version suffix from Ensembl IDs

Usage

removeEnsemblVersion(ensemblIDs)

Arguments

ensemblIDs

A vector of character strings. Other types of inputs are converted.

Value

A character vector of the same length as input

Examples

ensemblIDs <- c("ENSG00000197535", "ENST00000399231.7", "ENSP00000418960.2")
removeEnsemblVersion(ensemblIDs)

---

Construct a JSON string to indicate returned fields from a MongoDB query

Description

Construct a JSON string to indicate returned fields from a MongoDB query

Usage

returnFieldsJson(fields, include_id = FALSE)

Arguments

fields	A vector of character strings that should be included
include_id	Logical, whether _id should be returned. Default is FALSE

Value

A JSON string that represents the fields to be returned

Examples

returnFieldsJson(c("name", "birthday"))
returnFieldsJson(c("name", "birthday"), include_id=TRUE)

---

Locate ribiosAnnotation secrets file in JSON

Description

ribiosAnnotation needs to access databases to fetch annotations, the process of which requires credentials for these databases. The package looks for a file in JSON format, either specified in environment variable RIBIOS_ANNOTATION_SECRETS_JSON, or in the file ‘~/.credentials/ribiosAnnotation-secrets.json’, which contains the credentials. If this file is not found, no queries can be made.

Usage

ribiosAnnotationSecretEnvVar

locateSecretsFile(path)

Arguments

path	Path to the secret file. If not set, in case the environmental variable RIBIOS_ANNOTATION_SECRETS_JSON is set, its value is used as the file path; if not, ‘~/.credentials/ribiosAnnotation-secrets.json’ is used. In any case, if the file does not exist, a message will be printed.

Format

An object of class character of length 1.

Details

The function locates the file and returns the normalized path of the file.

Value

String, the normalized path of the file

---

ribiosAnnotation secret file

Description

ribiosAnnotation secret file

Usage

ribiosAnnotationSecretFile

Format

An object of class character of length 1.

---

Sort the annotation table by query IDs

Description

Sort the annotation table by query IDs

Usage

sortAnnotationByQuery(anno, ids, id_column = "GeneID", multi = FALSE)

Arguments

anno	A data.frame containing annotations
ids	A vector of character or integer, identifiers used to query the annotation
id_column	Character, column of the data frame where ids can be found.
multi	In case that an identifier appears more than once in id_column, should all rows be returned or only the first row? Default: FALSE, namely only the first row is returned.

Value

A data.frame sorted by the query identifiers, with the column id_column containing exactly the same value as ids. If the identifiers are unique and if they do not contain NA, they are used as the row names of the data.frame; otherwise, NULL will be used.

Examples

myAnno <- data.frame(GeneID=c(4,6,5), GeneName=c("Gene4", "Gene6", "Gene5"))
inputIds <- c("6", "5", "6", "4", "NotAGeneID")
sortAnnotationByQuery(myAnno, inputIds, "GeneID")

myAnno2 <- data.frame(GeneID=c(4,6,5, 5), 
                      GeneName=c("Gene4", "Gene6", "Gene5", "Gene5.V2"))
inputIds <- c("6", "5", "6", "4", "NotAGeneID")
sortAnnotationByQuery(myAnno2, inputIds, "GeneID")
sortAnnotationByQuery(myAnno2, inputIds, "GeneID", multi=TRUE)

---

Get Uniprot annotation with NCBI Taxonomy ID

Description

Get Uniprot annotation with NCBI Taxonomy ID

Usage

uniprotByTaxID(taxid, orthologue = FALSE, multiOrth = FALSE)

Arguments

taxid	NCBI Taxonomy ID
orthologue	Logical, whether human orthologues should be appended to the annotation
multiOrth	Logical, whether to return all orthologues or the (randomly) selected top one if multiple exist. Only valid when orthologue is set as TRUE.

Value

A data.frame with UniProt accessions and gene annotations.

See Also

* annotateUniprotAccession, which annotates Uniprot accessions * annotateTaxID, which annotates genes given TaxID.

Examples

## Not run: 
humanUniprot <- uniprotByTaxID(9606)

## End(Not run)

---

Return valid features in a vector

Description

Return valid features in a vector

Usage

validFeatureIDs(featureIDs)

Arguments

featureIDs

A vector of character strings

Value

A filtered vector containing only valid feature IDs.

Factor input will remain factors as output, but with invalid levels dropped. The output class will remain the same in case of integer or character input.

See Also

isValidFeatureID

Examples

featureIDs <- c("AMPK", "", "ACTB", "-")
validFeatureIDs(featureIDs)

---