get_deg_all: get_deg_all

In tinyarray: Expression Data Analysis and Visualization

get_deg_all

Description

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

Usage

get_deg_all(
  exp,
  group_list,
  ids = NULL,
  symmetry = TRUE,
  my_genes = NULL,
  show_rownames = FALSE,
  cluster_cols = TRUE,
  color_volcano = c("#2874C5", "grey", "#f87669"),
  logFC_cutoff = 1,
  pvalue_cutoff = 0.05,
  adjust = TRUE,
  entriz = TRUE,
  n_cutoff = 2,
  annotation_legend = FALSE,
  lab = NA,
  change_col = "change",
  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	logical,show rownames or not
cluster_cols	boolean values determining if columns should be clustered or hclust object.
color_volcano	color for volcano
logFC_cutoff	Cutoff value of logFC,1 by default.
pvalue_cutoff	Cutoff value of pvalue,0.05 by default.
adjust	a logical value; if TRUE, use padj and plot -log10(padj); otherwise use P.value and plot -log10(P.value).
entriz	logical, if TRUE, convert symbols to Entrez IDs.
n_cutoff	numeric cutoff used after scaling; values outside [-n_cutoff, n_cutoff] are truncated before plotting.
annotation_legend	logical,show annotation legend or not
lab	label for x axis in volcano plot; when 'NA', pkg = 4 uses 'log2FoldChange', and the other package codes keep their original labels
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.
species	choose human, mouse, or rat; default is human

Value

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

Author(s)

Xiaojie Sun

See Also

get_deg;multi_deg_all

Examples

## Not run: 
if(requireNamespace("Biobase",quietly = TRUE)&
   requireNamespace("AnnoProbe",quietly = TRUE)){
  gse = "GSE42872"
  geo = geo_download(gse,destdir=tempdir())
  group_list = rep(c("A","B"),each = 3)
  group_list = factor(group_list)
  find_anno(geo$gpl)
  ids <- AnnoProbe::idmap(geo$gpl,destdir = tempdir())
  dcp = get_deg_all(geo$exp,group_list,ids,entriz = FALSE)
  head(dcp$deg)
  dcp$plots
}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.