NEWS

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gage 2.47.1

• korg now include 8282 KEGG species or 1449 new species beyond 2020.
• updated khier to included newly added reference pathways. kegg.gsets can work with 477 pathways now.

gage 2.41.1

• korg now include 6833 KEGG species or 1588 new species beyond 2017.
• updated khier to included newly added reference pathways. kegg.gsets can work with 466 pathways now.
• fixed installation and checking error by removing suggesting the deprectated DESeq.

gage 2.39.3

• fixed warning on "library(GO.db)" in go.gsets.R. Now "import" from GO.db, instead of "suggest" it.

gage 2.39.2

• fixed error caused by class(exprs) == "data.frame" in gagePrep.R. class(exprs) now returns a vector of length 2, which caused the error.

gage 2.28.2

• korg now include 5245 KEGG species. In addition an updated version of korg is now checked out from Pathview Web server by loading .rda file (inst4ead of read .tsv file) when needed.

gage 2.27.3

• fixed bug in kegg.gsets function, which cause error when species="ko" (KEGG Orthology).

gage 2.27.1

• major expansion in korg, which now include both KEGG and NCBI taxonomy IDs, two more gene ID types, i.e. NCBI protein and uniprot IDs. In addition, Entrez or NCBI Gene IDs are discontinued for most prokaryotes.
• korg now include 4800 KEGG species, in the meantime, an updated version of korg is now checked out from Pathview Web server each R session when kegg.gsets function is called the first time. version 2.20.1
• updated RNA-seq workflow vignette, especially step 1 summarizeOverlaps, and correct tophat web link. version 2.19.1
• updated gage main vignette and RNA-seq workflow vignette. Add reminder on species and gene ID data consistence check to the former, and correct Cufflinks output format and web link. version 2.17.2
• updated khier to included newly added reference pathways. kegg.gsets can work with 397 pathways now. version 2.15.5
• updated korg to included over 80 newly added species, such as sheep, apple, mandarin orange etc. Pathview can work with 3050 species now. version 2.14.3
• revised the internal function gs.heatmap as to allow margin sizes ajustment for gene set heatmaps directly or through sigGeneSet. version 2.14.1
• revised "RNA-Seq Data Pathway and Gene-set Analysis Workflows" to reflect summarizeOverlaps() migration to GenomicAlignments package for Bioc 2.14. version 2.13.5
• add function go.gsets, which generates up-to-date GO gene sets for 19 common species annotated in Bioconductor and more others by the users. version 2.13.3 (2.12.3)
• updated korg to included over 600 newly added species. kegg.gsets can work with 2970 species now.
• fixed typos in joint workflows with Cufflinks (page 13): range(exp.fc) to range(cuff.fc) version 2.12.2
• fixed typos in joint workflows with DESeq2 (page 11): cnts.kegg.p should be fc.kegg.p

gage 2.12.1

• remove pathview from the imports list for easier installation and loading.

gage 2.11.3

• add secondary vignette, "RNA-Seq Data Pathway and Gene-set Analysis Workflows".
• add function kegg.gsets, which generates up-to-date KEGG pathway gene sets for any specified KEGG species.

gage 2.9.4

• add secondary vignette, "Gene set and data preparation", on data preparation.

gage 2.9.2

• suggests and connected to pathview package for results visualization.

gage 2.9.1

• removed dependency on multtest package for p-value FDR adjustment, use p.adjust function of the stat package instead.
• change "depends" to "imports" for graph package as we only need to import graphNEL class and connComp method.
• subset kegg.gs. From now, kegg.gs only include the subset of canonical signaling and metabolic pathways from KEGG pathway database, and kegg.gs.dise is the subset of disease pathways. And it is recommended to do KEGG pathway analysis with either kegg.gs or kegg.gs.dise seperately (rather than combined altogether) for better defined results. Note that kegg.gs and subsets are be defined slightly different in gageData package.
• In gage vignette, add citation section and an example of including all genes (rather than those selected using essGene function) in top gene set result check using geneData function.

gage 2.2.0

• More robust p-value summarization using Stouffer's method through argument use.stouffer=TRUE. The original p-value summarization, i.e. negative log sum following a Gamma distribution as the Null hypothesis, may produce less stable global p-values for large or heterogenous datasets. In other words, the global p-value could be heavily affected by a small subset of extremely small individual p-values from pair-wise comparisons. Such sensitive global p-value leads to the "dual signficance" phenomenon. Dual-signficant means a gene set is called significant simultaneously in both 1-direction tests (up- and down-regulated). "Dual signficance" could be informative in revealing the sub-types or sub-classes in big clinical or disease studies, but may not be desirable in other cases.
• Output of gage function now includes the gene set test statistics from pair-wise comparisons for all proper gene sets. The output is always a named list now, with either 3 elements ("greater", "less", "stats") for one-directional test or 2 elements ("greater", "stats") for two-directional test.
• The individual p-value (and test statistics)from dependent pair-wise comparisions, i.e. comparisions between the same experiment vs different controls, are now summarized into a single value. In other words, the column number of individual p-values or statistics is always the same as the sample number in the experiment (or disease) group. This change made the argument value compare="1ongroup" and argument full.table less useful. It also became easier to check the perturbations at gene-set level for individual samples.
• Whole gene-set level changes (either p-values or statistics) can now be visualized using heatmaps due to the third change above. Correspondingly, functions \code{sigGeneSet} and \code{gagePipe} have been revised to plot heatmaps for whole gene sets.
• Fixed a bug in gs.zTest function: mod <- (length(ix)/s)^(1/2), it is mod <- length(ix)^(1/2)/s before. Thanks to Nhan Thi HO from Michigan State University.