multi_deg: multi_deg

In tinyarray: Expression Data Analysis and Visualization

multi_deg

Description

do diffiential analysis according to expression set and group information

Usage

multi_deg(
  exp,
  group_list,
  ids,
  logFC_cutoff = 1,
  pvalue_cutoff = 0.05,
  adjust = FALSE,
  species = "human",
  entriz = TRUE
)

Arguments

exp	A numeric matrix
group_list	A factor with duplicated character or factor
ids	a data.frame with 2 columns,including probe_id and symbol
logFC_cutoff	Cutoff value of logFC,1 by default.
pvalue_cutoff	Cutoff value of pvalue,0.05 by default.
adjust	a logical value, would you like to use adjusted pvalue to draw this plot,FAlSE by default.
species	choose human or mouse, or rat, default: human
entriz	whether convert symbols to entriz ids

Value

a deg data.frame with 10 columns

Author(s)

Xiaojie Sun

See Also

get_deg;multi_deg_all

Examples

## Not run: 
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$gpl,destdir = tempdir())
deg = multi_deg(geo$exp,group_list,ids,adjust = FALSE)
names(deg)
head(deg[[1]])
head(deg[[2]])
head(deg[[3]])

## End(Not run)

tinyarray documentation built on Aug. 18, 2023, 9:07 a.m.