rem_mv {MetaVolcanoR} | R Documentation

## A function to perform the Random Effect Model (REM) MetaVolcano

### Description

This function runs the 'Random Effect Model' MetaVolcano section

### Usage

    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

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

[Package MetaVolcanoR version 1.2.0 Index]