Rank-based tests for enrichment of KOG (euKaryotic Orthologous Groups) classes with up- or down-regulated genes based on a continuous measure. The meta-analysis is based on correlation of KOG delta-ranks across datasets (delta-rank is the difference between mean rank of genes belonging to a KOG class and mean rank of all other genes). With binary measure (1 or 0 to indicate significant and non-significant genes), one-tailed Fisher's exact test for over-representation of each KOG class among significant genes will be performed.
|Author||Mikhail V. Matz|
|Date of publication||2016-11-17 08:27:29|
|Maintainer||Mikhail V. Matz <email@example.com>|
adults.3dHeat.logFoldChange: Heat stress response of adult coral
corrPlot: Plots a pairwise correlation with linear regression line
gene2kog: KOG class annotations
kog.ft: One-tailed Fisher's exact test for KOG enrichment.
kog.mwu: Tests for KOG class enrichment.
KOGMWU-package: Functional summary and meta-analysis of gene expression data
kog.mwut: Mann-Whitney U test for KOG enrichment.
larvae.longTerm: Long-term heat stress response of coral larvae
larvae.shortTerm: Short-term heat stress response of coral larvae
makeDeltaRanksTable: Make a combined delta-ranks table from several kog.mwu()...
panel.cor: accessory function for pairs() to display Pearson...
panel.cor.pval: accessory function for pairs() to display pvalue of the...