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

Description Usage Arguments Value Examples

View source: R/combining_mv.R

Description

This function draws the 'Combining meta-analysis' MetaVolcano

Usage

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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

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