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

Description Usage Arguments Value Examples

View source: R/votecount_mv.R

Description

This function draws the vote-counting meta-analysis MetaVolcano

Usage

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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

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MetaVolcanoR documentation built on April 29, 2020, 2:08 a.m.