create_DEseq: create_DEseq

In Feng-Zhang/RNAseqFlow:

create_DEseq

Description

This function would generate a object of DESeq2 class

Usage

create_DEseq(
  count_data,
  col_data,
  design_names = "condition+type",
  group_name = "condition",
  ref_level = "control"
)

Arguments

count_data	a matrix with row name
col_data	a dataframe include group information
design_names	designs with multiple variables, e.g., group + condition, and designs with interactions, e.g., genotype + treatment + genotype:treatment.
group_name	the name of col_data to split case and control group
ref_level	a character which is the reference group

Value

a list

Examples

## Not run: 
input = createCountPhe()
dds = DEseqObj(input[[1]],input[[2]],ref_level="untreated")

## End(Not run)

Feng-Zhang/RNAseqFlow documentation built on Sept. 10, 2022, 7:13 a.m.