combining_mv: A function to draw the 'Combining meta-analysis' MetaVolcano

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

Description

This function draws the 'Combining meta-analysis' MetaVolcano

Usage

combining_mv(diffexp = list(), pcriteria = "pvalue",
  foldchangecol = "Log2FC", genenamecol = "Symbol", geneidcol = NULL,
  metafc = "Mean", 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 c("adj.P.Val", "P.Value") <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>
metafc	method for summarizing gene fold-changes across studies c("Mean", "Median") <string>
metathr	top percentage of perturbed genes to be highlighted <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 the .pdf or .html visualization <c(NULL, "PDF", "HTML")>

Value

MetaVolcano object

Examples

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

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