KOGMWU: Functional Summary and Meta-Analysis of Gene Expression Data
Version 1.1

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.

AuthorMikhail V. Matz
Date of publication2016-11-17 08:27:29
MaintainerMikhail V. Matz <matz@utexas.edu>
LicenseGPL-3
Version1.1
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("KOGMWU")

Getting started

Package overview

Popular man pages

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.
kog.mwut: Mann-Whitney U test for KOG enrichment.
larvae.shortTerm: Short-term heat stress response of coral larvae
panel.cor: accessory function for pairs() to display Pearson...
See all...

All man pages Function index File listing

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...

Functions

KOGMWU Man page
KOGMWU-package Man page
adults.3dHeat.logFoldChange Man page
corrPlot Man page Source code
gene2kog Man page
kog.ft Man page Source code
kog.mwu Man page Source code
kog.mwut Man page Source code
larvae.longTerm Man page
larvae.shortTerm Man page
makeDeltaRanksTable Man page Source code
panel.cor Man page Source code
panel.cor.pval Man page Source code

Files

NAMESPACE
data
data/larvae.longTerm.rda
data/gene2kog.rda
data/larvae.shortTerm.rda
data/datalist
data/adults.3dHeat.logFoldChange.rda
R
R/panel.cor.R
R/panel.cor.pval.R
R/kog.ft.R
R/makeDeltaRanksTable.R
R/kog.mwu.R
R/kog.mwut.R
R/corrPlot.R
MD5
DESCRIPTION
man
man/makeDeltaRanksTable.Rd
man/adults.3dHeat.logFoldChange.Rd
man/larvae.longTerm.Rd
man/kog.ft.Rd
man/KOGMWU-package.Rd
man/kog.mwu.Rd
man/kog.mwut.Rd
man/panel.cor.Rd
man/corrPlot.Rd
man/gene2kog.Rd
man/panel.cor.pval.Rd
man/larvae.shortTerm.Rd
KOGMWU documentation built on May 19, 2017, 9:39 a.m.

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