rem_mv: A function to perform the Random Effect Model (REM)...
In csbl-usp/MetaVolcanoR: Gene Expression Meta-analysis Visualization Tool

Description Usage Arguments Value Examples

This function runs the 'Random Effect Model' MetaVolcano section

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)

`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>

MetaVolcano object

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