NEWS

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ribiosGSEA 1.3-2 (2016-12-22)

• add ronetGGI to query gene-gene interactions from RONET
• officially move geeSetPerm from ribiosGSA to ribiosGSEA

ribiosGSEA 1.1-8

• The GeneSet class and GeneSets class are re-designed to support the concept of 'category', namely classes of gene sets. The old class 'GeneSetsList' is removed because its functionality is represented by GeneSets (which provides even more functionality)
• Add FisherResult and FisherResultList objects to support Fisher's exact test based gene set enrichment analysis
• readGmt now combines readGmt and readGmts, supporting simultaneous reading of several gmt files
• Remove 'geneCountFilter' function and replace with 'filterBySize' S4 generic
• Improved functionality of working with GeneSets

ribiosGSEA 1.1-7

• GSEA file directory changes according to the new server setup

ribiosGSEA 1.1-6

• Clean up importing/depending packages: only methods is depended and other packages are all imported
• Add GeneSetsList, a list of GeneSets, to allow simultaneous testing of gene sets in multiple gmt files
• Add readGmts

ribiosGSEA 1.1-5

• Add gseaScore and gseaScores function to extract scores from annoGseaRes object(s)

ribiosGSEA 1.1-4

• Add parseGmt function to transform a GMT file into a list of integer indices that is directly applicable for downstream analysis

ribiosGSEA 1.1-3

• Remove mroast2tbl since the latest version of limma is already returning a data.frame
• add gmthyper and gmthyperList functions to perform Fisher test with GMT files
• clean up gseaES and gseaQvalue functions

ribiosGSEA 1.1-2

• Bug fix in matchGenes and geneCounts.

ribiosGSEA 1.1-1

• parseGSEA functions are added to parse all relevant information from a GSEA output directory
• gsName, gsDesc, and gsGenes are harmonized for both GSEA results parsing and general GMT file parsing
• Classes and methods are added to handle gene sets and GSEA results

ribiosGSEA 1.0-9

• Variables such as GSEA_GENESET_DIR are exported.

ribiosGSEA 1.0-8

• gseaFingerprint.Rscript does not warn when -sortBy is not specified

ribiosGSEA 1.0-7

• Add list2mat, transforming first-level lists to adjacency matrix
• ntpTemplates are updated so that it directly inherits a matrix

ribiosGSEA 1.0-6

• Add function ntp to implement the Nearest Template Prediction Algorithm
• Add functions readGmt, gsNames, gsDescs, gsGenes, geneCountFilter, etc. to manipulate GeneSets objects from GMT files
• Add ntpTemplates and ntpBiTemplates to construct NTP-templates from GeneSets.

ribiosGSEA 1.0-5

• New feature of gmtIndices: invalid Gene Symbols ("", "-") are removed

ribiosGSEA 1.0-4

• New function added, mroast2tbl, to reformat result lists of limma::mroast into data frame.
• New function added, gmtIndices.Rd, to get integer indices of genes in GMT gene set lists from a vector of gene symbols. Used by functions such as 'mroast' and 'camera' in the limma package.
• New function added, filterGmtByGeneCount, to filter gmt lists by gene counts.
• Improvement of buildGSEAcomm: CHIP_FILE is no longer a mandatory parameter. When the option is missing, the GSEA tool performs no mapping between rnk-file identifiers and GMT-file identifiers, for instance when both files use official gene symbols.

ribiosGSEA 1.0-3

• gseaFingerprint is now able to deal with cases where the phenotypes are now named in default as 'pos' and 'neg'. Since in such cases, the order of positive/negative is not clearly defined, we use the alphabetic order of phenotype names as 'pos' and 'neg'.

ribiosGSEA 1.0-2

• gseaFingerprintMatrix: omit empty directories
• gseaFingerprintMatrix: stops if all input directories are detected NOT to be GSEA result folders
• gseaQvalue: q-values is given in -log10(p) instead of -log(p) (base-10) to make interpretation easier
• Add buildGSEAcomm: build bash commands to run GSEA. Able to deal with irregular file names

ribiosGSEA 1.0-1

• gseaFingerprints.Rscript: remove empty lines from input file

ribiosGSEA 1.0-0

• Establish the ribiosGSEA package
• Refactor GSEA-related functions from other packages
• Add functions used to extract fingerprints from GSEA results