twoGroupDEgenes: DE genes analysis for two groups.

In Tong-Chen/YSX: For Yishengxin Training

Description

DE genes analysis for two groups.

Usage

twoGroupDEgenes(
  dds,
  groupA,
  groupB,
  design = "conditions",
  padj = 0.05,
  log2FC = 1,
  dropCol = c("lfcSE", "stat"),
  output_prefix = "ehbio",
  ...
)

Arguments

dds	DESeq function returned object.
groupA	Group name 1.
groupB	Group name 2.
design	The group column name. Default "conditions".
padj	Multiple-test corrected p-value. Default 0.05.
log2FC	Log2 transformed fold change. Default 1.
dropCol	Columns to drop in final output. Default c("lfcSE", "stat"). Other options "ID", "baseMean", "log2FoldChange", "lfcSE", "stat", "pvalue", "padj". This has no specific usages except make the table clearer.
output_prefix	A string as prefix of output files.
...	Additional parameters given to ggsave.

Examples

twoGroupDEgenes(dds, "trt", "untrt")

Tong-Chen/YSX documentation built on Jan. 25, 2021, 2:49 a.m.