KOGMWU: Functional Summary and Meta-Analysis of Gene Expression Data

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 <matz@utexas.edu>
License
GPL-3
Version
1.1

View on CRAN

Man pages

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...

Files in this package

KOGMWU
KOGMWU/NAMESPACE
KOGMWU/data
KOGMWU/data/larvae.longTerm.rda
KOGMWU/data/gene2kog.rda
KOGMWU/data/larvae.shortTerm.rda
KOGMWU/data/datalist
KOGMWU/data/adults.3dHeat.logFoldChange.rda
KOGMWU/R
KOGMWU/R/panel.cor.R
KOGMWU/R/panel.cor.pval.R
KOGMWU/R/kog.ft.R
KOGMWU/R/makeDeltaRanksTable.R
KOGMWU/R/kog.mwu.R
KOGMWU/R/kog.mwut.R
KOGMWU/R/corrPlot.R
KOGMWU/MD5
KOGMWU/DESCRIPTION
KOGMWU/man
KOGMWU/man/makeDeltaRanksTable.Rd
KOGMWU/man/adults.3dHeat.logFoldChange.Rd
KOGMWU/man/larvae.longTerm.Rd
KOGMWU/man/kog.ft.Rd
KOGMWU/man/KOGMWU-package.Rd
KOGMWU/man/kog.mwu.Rd
KOGMWU/man/kog.mwut.Rd
KOGMWU/man/panel.cor.Rd
KOGMWU/man/corrPlot.Rd
KOGMWU/man/gene2kog.Rd
KOGMWU/man/panel.cor.pval.Rd
KOGMWU/man/larvae.shortTerm.Rd