rem_mv: A function to perform the Random Effect Model (REM)...

Description Usage Arguments Value Examples

View source: R/rem_mv.R

Description

This function runs the 'Random Effect Model' MetaVolcano section

Usage

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rem_mv(diffexp = list(), pcriteria = "pvalue",
  foldchangecol = "Log2FC", genenamecol = "Symbol", geneidcol = NULL,
  collaps = FALSE, llcol = "CI.L", rlcol = "CI.R", vcol = NULL,
  cvar = TRUE, metathr = 0.01, jobname = "MetaVolcano",
  outputfolder = ".", draw = "HTML", ncores = 1)

Arguments

diffexp

list of data.frame/data.table (s) with DE results where lines are genes

pcriteria

the column name of the pvalue variable <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>

collaps

if probes should be collapsed based on the DE direction <logical>

llcol

left limit of the fold change coinfidence interval variable name <string>

rlcol

right limit of the fold change coinfidence interval variable name <string>

vcol

name of the fold change variance variable <string>

cvar

weather or not to calculate gene variance from confidence interval limits <logical>

metathr

top percentage of perturbed genes to be highlighted <double>

jobname

name of the running job <string>

outputfolder

/path where to write the results/

draw

wheather or not to draw the .html visualization <logical>

ncores

the number of processors the user wants to use <integer>

Value

MetaVolcano object

Examples

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data(diffexplist)
diffexplist <- lapply(diffexplist, function(del) {
    dplyr::filter(del, grepl("MP", Symbol))
})
mv <- rem_mv(diffexplist, metathr = 0.1)
str(mv)

MetaVolcanoR documentation built on Nov. 8, 2020, 7:52 p.m.