plotCounts: Plot of normalized counts for a single gene on log scale

In nlhuong/ZeroInflatedDESeq2: Differential gene expression analysis based on the negative binomial distribution

Description

Note: normalized counts plus a pseudocount of 0.5 are shown.

Usage

plotCounts(dds, gene, intgroup = "condition", normalized = TRUE,
  transform = FALSE, main, xlab = "group", returnData = FALSE,
  replaced = FALSE, ...)

Arguments

dds	a DESeqDataSet
gene	a character, specifying the name of the gene to plot
intgroup	interesting groups: a character vector of names in colData(x) to use for grouping
normalized	whether the counts should be normalized by size factor (default is TRUE)
transform	whether to present log2 counts (TRUE) or to present the counts on the log scale (FALSE, default)
main	as in 'plot'
xlab	as in 'plot'
returnData	should the function only return the data.frame of counts and covariates for custom plotting (default is FALSE)
replaced	use the outlier-replaced counts if they exist
...	arguments passed to plot

Examples

dds <- makeExampleDESeqDataSet()
plotCounts(dds, "gene1")

nlhuong/ZeroInflatedDESeq2 documentation built on May 23, 2019, 9:06 p.m.