plotBarCodes: Perform ROAST and make BarCodePlot using a voom transformed...

In vivekbhr/vivlib: An R package for useful bioinformatics wrappers

Description

This function was originally written for comparing a voom-transformed mouse input and a microarry (affy) input from human or mouse. That's why the option to provide a Human-Mouse ID map. But if you don't want that, you can simply use it to compare any set of microarry outputs to any voom-transformed input.

Usage

plotBarCodes(GSEfile, ourVoomFile, batchAnalyse = TRUE,
  VoomInputName = NULL, humanMouseNameMap = NULL, dfCutoff = "pvalue",
  logFoldCh = 0, padj = 0.05, outFolder = NULL)

Arguments

GSEfile	A microarry data file. Filename should start from 'GSE'. The columns should have 'gname' and 'SPOT_ID'.
ourVoomFile	Voom transformed output from makeVoomInput
batchAnalyse	If there are multiple microarry files in the folder, give the folder path.
VoomInputName	Provide a name for our Voom-transformed input data.
humanMouseNameMap	A tab-seperated file with column ("Sym_Human") which provides alternative human symbol for our mouse gene IDs
dfCutoff	Which cutoff to use for filtering genes from GSEfile. Default is by pvalue. Otherwise a log Fold Change cutoff can be used.
logFoldCh	logFoldChange cutoff for filtering GSE file (if used)
padj	adjusted p-value cutoff for filtering GSE file (if used)
outFolder	Folder to write the output pdf file.

Value

Pdf file with barcode plots

Examples

## Not run: 
     plotBarCodes(GSEfile,ourVoomFile)

## End(Not run)

vivekbhr/vivlib documentation built on May 3, 2019, 6:13 p.m.