votecount_mv: A function to draw the 'Vote-counting meta-analysis'...

In csbl-usp/MetaVolcanoR: Gene Expression Meta-analysis Visualization Tool

Description

This function draws the vote-counting meta-analysis MetaVolcano

Usage

votecount_mv(diffexp = list(), pcriteria = "pvalue",
  foldchangecol = "Log2FC", genenamecol = "Symbol", geneidcol = NULL,
  pvalue = 0.05, foldchange = 0, metathr = 0.01, collaps = FALSE,
  jobname = "MetaVolcano", outputfolder = ".", draw = "HTML")

Arguments

diffexp	list of data.frame/data.table (s) with DE results where lines are genes
pcriteria	the column name of the Pval criteria to consider <string>
foldchangecol	the column name of the foldchange variable <string>
genenamecol	the column name of the gene name variable <string>
geneidcol	the column name of the gene ID/probe/oligo/transcript variable <string>
pvalue	the Pval to use as threshold c(0:1) <double>
foldchange	the foldchange to use as DE threshold c(-Inf: Inf) <double>
metathr	the proportion of studies a gene has to be DEG to be considered cDEG <double>
collaps	if probes should be collapsed based on the DE direction <logical>
jobname	name of the running job <string>
outputfolder	/path where to write the results/
draw	wheather or not to draw a .pdf or .html visualization <c(NULL, 'PDF', 'HTML')>

Value

MetaVolcano object

Examples

data(diffexplist)
mv <- votecount_mv(diffexplist)
str(mv)

csbl-usp/MetaVolcanoR documentation built on Nov. 8, 2019, 8:53 p.m.