degQC: Plot main figures showing p-values distribution and...
In lpantano/DEGreport: Report of DEG analysis

degQC

R Documentation

Plot main figures showing p-values distribution and mean-variance correlation

Description

This function joins the output of degMean, degVar and degMV in a single plot. See these functions for further information.

Usage

degQC(counts, groups, object = NULL, pvalue = NULL)

Arguments

`counts`	Matrix with counts for each samples and each gene.
`groups`	Character vector with group name for each sample in the same order than counts column names.
`object`	DEGSet oobject.
`pvalue`	pvalues of DEG analysis.

Value

ggplot2 object

Examples

data(humanGender)
library(DESeq2)
idx <- c(1:10, 75:85)
dds <- DESeqDataSetFromMatrix(assays(humanGender)[[1]][1:1000, idx],
  colData(humanGender)[idx,], design=~group)
dds <- DESeq(dds)
res <- results(dds)
degQC(counts(dds, normalized=TRUE), colData(dds)[["group"]],
  pvalue = res[["pvalue"]])

lpantano/DEGreport documentation built on Feb. 28, 2024, 12:01 a.m.