DEGAnalysis_DESeq2: DEG analysis using samples with replicates.

In biomarble/PlantNGSTools: NGS bioinformatics tools for plants

DEG analysis using samples with replicates.

Description

do DEG analysis using samples with replicates by DESeq2.

Usage

DEGAnalysis_DESeq2(
  countMatrix,
  group,
  useFDR = F,
  cut = 0.05,
  FCcut = 2,
  control = "Manually_select",
  treat = "Manually_select",
  outdir = NULL
)

Arguments

countMatrix	input count matrix, rows are genes and columns are samples
group	group dataframe, first column: sample ID, second column: group name
useFDR	whether to use FDR to define significant DEG
cut	significant P value threshold, is useFDR is set , FDR is used
FCcut	Fold Change threshold
control	control group name, used as denominator in Fold Change calculation
treat	treat group name, used as numerator in Fold Change calculation
outdir	output file directory

biomarble/PlantNGSTools documentation built on Feb. 8, 2024, 2:46 a.m.