get_deg_all: get_deg_all

In tinyarray: Expression Data Analysis and Visualization

get_deg_all

Description

do diffiencial analysis according to exprission set and group information

Usage

get_deg_all(
  exp,
  group_list,
  ids,
  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 = FALSE,
  entriz = TRUE,
  n_cutoff = 2,
  annotation_legend = FALSE,
  lab = NA,
  species = "human"
)

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
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, would you like to use adjusted pvalue to draw this plot,FAlSE by default.
entriz	logical , if TRUE ,convert symbol to entriz id.
n_cutoff	3 by defalut , scale before plot and set a cutoff,usually 2 or 1.6
annotation_legend	logical,show annotation legend or not
lab	label for x axis in volcano plot, if NA , x axis names by package
species	choose human or mouse, or rat, default: human

Value

a list with 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: 
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$exp,group_list,ids)
head(dcp$deg)
dcp$plots

## End(Not run)

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