multi_deg_all: multi_deg_all
In tinyarray: Expression Data Analysis and Visualization

multi_deg_all

R Documentation

multi_deg_all

Description

Do differential analysis according to an expression set and group information.

Usage

multi_deg_all(
  exp,
  group_list,
  ids = NULL,
  symmetry = TRUE,
  my_genes = NULL,
  show_rownames = FALSE,
  cluster_cols = TRUE,
  color_volcano = c("#2874C5", "grey", "#f87669"),
  pvalue_cutoff = 0.05,
  logFC_cutoff = 1,
  adjust = TRUE,
  entriz = TRUE,
  change_col = "change",
  annotation_legend = FALSE,
  lab = NA,
  species = "human"
)

Arguments

`exp`	A numeric matrix
`group_list`	A character or factor vector with one label per sample; character input will be converted to factor and unused levels will be dropped.
`ids`	optional probe-to-symbol annotation table. If 'NULL', 'exp' is treated as a gene-level matrix and no ID conversion is performed.
`symmetry`	a logical value ,would you like to get your plot symmetrical
`my_genes`	genes for pheatmap
`show_rownames`	boolean specifying if column names are be shown.
`cluster_cols`	boolean values determining if columns should be clustered or `hclust` object.
`color_volcano`	color for volcano
`pvalue_cutoff`	Cutoff value of pvalue,0.05 by default.
`logFC_cutoff`	Cutoff value of logFC,1 by default.
`adjust`	a logical value; if TRUE, use `padj` and plot `-log10(padj)`; otherwise use `P.value` and plot `-log10(P.value)`.
`entriz`	whether to convert symbols to Entrez IDs
`change_col`	column name for the up/down/status label. Default uses 'change' when it exists; otherwise the function falls back to the existing automatic classification logic.
`annotation_legend`	boolean value showing if the legend for annotation tracks should be drawn.
`lab`	label for x axis in volcano plot; when 'NA', pkg = 4 uses 'log2FoldChange', and the other package codes keep their original labels
`species`	choose human, mouse, or rat; default is human

Value

a list with deg data.frame, volcano plot and a list with DEGs.

Author(s)

Xiaojie Sun

Examples

## Not run: 
if(requireNamespace("Biobase",quietly = TRUE)&
   requireNamespace("AnnoProbe",quietly = TRUE)){
gse = "GSE474"
geo = geo_download(gse,destdir=tempdir())
geo$exp[1:4,1:4]
geo$exp=log2(geo$exp+1)
group_list=ifelse(stringr::str_detect(geo$pd$title,"MObese"),"MObese",
ifelse(stringr::str_detect(geo$pd$title,"NonObese"),"NonObese","Obese"))
group_list=factor(group_list,levels = c("NonObese","Obese","MObese"))
find_anno(geo$gpl)
ids = AnnoProbe::idmap(geo$gpl,destdir = tempdir())
dcp = multi_deg_all(geo$exp,
group_list,ids,adjust = FALSE,entriz = FALSE)
dcp[[3]]
}else{
  if(!requireNamespace("AnnoProbe",quietly = TRUE)) {
    warning("Package 'AnnoProbe' needed for this function to work.
         Please install it by install.packages('AnnoProbe')",call. = FALSE)
  }
  if(!requireNamespace("Biobase",quietly = TRUE)) {
    warning("Package 'Biobase' needed for this function to work.
         Please install it by BiocManager::install('Biobase')",call. = FALSE)
  }
}

## End(Not run)

tinyarray documentation built on Aug. 2, 2026, 9:07 a.m.