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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.

Functions (12)

KOGMWU-package

Functional summary and meta-analysis of gene expression data

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.

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() results.

panel.cor

accessory function for pairs() to display Pearson correlations

panel.cor.pval

accessory function for pairs() to display pvalue of the Pearson correlation

KOGMWU

Functional Summary and Meta-Analysis of Gene Expression Data

v1.2
GPL-3
Authors
Mikhail V. Matz
Initial release
2019-02-19

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