rem_mv {MetaVolcanoR} | R Documentation |
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)