run_DESeq2: DESeq2 wrapper

In Emask7/ZIKVtranscriptomics: ZIKV Transcriptomics Analyses

Description

DESeq2 wrapper

Usage

run_DESeq2(
  geneCounts,
  sample_data,
  expt_design,
  reduced_design,
  coefficient,
  contrast,
  min_lfc
)

Arguments

geneCounts	data.frame containing raw gene or transcript counts.
sample_data	data.frame containing experimental factors, with the number of rows equal to the number of samples
expt_design	a formula indicating the factors of the experimental design
reduced_design	a formula indicating the reduced version of expt_design (the factor of interest is removed)
coefficient	a number indicating the coefficient to be tested
contrast	a vector of strings indicating the factor and levels to be tested
min_lfc	minimum value of the absolute value of the LFC required to be significant

Examples

run_DESeq2(geneCounts, sample_data, expt_design, reduced_design, coefficient, contrast, min_lfc)

Emask7/ZIKVtranscriptomics documentation built on Jan. 25, 2022, 12:32 a.m.