get_cgs function

get_cgs

extract DEGs from deg data.frame

get_cgs(deg)

Arguments

• deg: a data.frame created by Differential analysis

Returns

a list with upgenes,downgenes,diffgenes.

Examples

## Not run:

#two group
gse = "GSE42872"
geo = geo_download(gse,destdir=tempdir())
group_list = rep(c("A","B"),each = 3)
ids = AnnoProbe::idmap('GPL6244',destdir=tempdir())
deg = get_deg(geo$exp,group_list,ids)
cgs = get_cgs(deg)
#mutigroup
gse = "GSE474"
geo = geo_download(gse,destdir=tempdir())
geo$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)
cgs = get_cgs(deg)
## End(Not run)

See Also

geo_download;draw_volcano;draw_venn

Author(s)

Xiaojie Sun