Random Effect Model (REM) MetaVolcano — rem

This function performs Random Effect Model meta-analysis on differential expression results. 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 = tempdir(),
  draw = "HTML",
  ncores = 1,
  colors = c(low = "#083e46", mid = "white", high = "#811820", na = "grey80"),
  point_size = 0.6,
  label_genes = NULL,
  label_top_n = NULL,
  label_size = 3,
  plot_title = NULL,
  show_legend = TRUE
  outputfolder = ".",
  draw = "HTML",
  ncores = 1,
  render = F
)

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>
colors: named vector of colors for gradient: c(low, mid, high, na)
point_size: size of points in the plot
label_genes: character vector of specific genes to label
label_top_n: number of top genes (by p-value) to label automatically
label_size: size of gene name labels
plot_title: custom plot title (NULL for no title)
show_legend: whether to show the legend (TRUE/FALSE)
ncores: the number of processors the user wants to use <integer> #' @param render A boolean parameter that determines whether the plot should be rendered. If `TRUE`, the function will produce and save the plot based on the specified `draw` parameter (either as an HTML or PDF file). If `FALSE` (default), no plot will be rendered or saved. It's useful for cases where you might want to run the function for its side effects or calculations without necessarily visualizing the result.

Value

MetaVolcano object

Examples

data(diffexplist)
diffexplist <- lapply(diffexplist, function(del) {
    dplyr::filter(del, grepl("MP", Symbol))
})