pathview_func: pathview_func (from pathview functions).

In ShirinG/exprAnalysis: A package for analysing RNA-seq and expression array data

Description

This produces pathview plots of differentially expressed genes and their fold changes for given pathways.

Usage

pathview_func(DEgenes, logFCcolumn = "logFC", pathway.id, out.suffix,
  organism = "human")

Arguments

DEgenes	List of differentially expressed genes as output given by diff_limma_pairwise(). Rownames should be gene names (SMYBOLS).
logFCcolumn	Name of column that contains log fold change information.
pathway.id	KEGG pathway identification number.
out.suffix	Output suffix to be added to file name.
organism	Set organism. Defaults to human, can also be mouse.

Details

If you get the error message(s) data set 'korg' not found and/or data set 'bods' not found, it didn't properly extract these datasets from the pathview package. Run data(korg) and data(bods) manually!

Value

Three output files are produced for each pathway: An .xml, a .png of the pathway and a .png of the pathway with DE genes and their fold change.

ShirinG/exprAnalysis documentation built on May 9, 2019, 1:28 p.m.