NEWS
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