metaseqR (version 1.12.2)

stat.bayseq: Statistical testing with baySeq

Description

This function is a wrapper over baySeq statistical testing. It accepts a matrix of normalized gene counts or an S4 object specific to each normalization algorithm supported by metaseqR.

Usage

stat.bayseq(object, sample.list, contrast.list = NULL,
        stat.args = NULL, libsize.list = NULL)

Arguments

object

a matrix or an object specific to each normalization algorithm supported by metaseqR, containing normalized counts. Apart from matrix (also for NOISeq), the object can be a SeqExpressionSet (EDASeq), CountDataSet (DESeq) or DGEList (edgeR).

sample.list

the list containing condition names and the samples under each condition.

contrast.list

a named structured list of contrasts as returned by make.contrast.list or just the vector of contrasts as defined in the main help page of metaseqr.

stat.args

a list of edgeR statistical algorithm parameters. See the result of get.defaults("statistics", "bayseq") for an example and how you can modify it.

libsize.list

an optional named list where names represent samples (MUST be the same as the samples in sample.list) and members are the library sizes (the sequencing depth) for each sample. If not provided, they will be estimated from baySeq.

Value

• A named list of the value 1-likelihood that a gene is differentially expressed, whose names are the names of the contrasts.

Examples

require(DESeq)
data.matrix <- counts(makeExampleCountDataSet())
sample.list <- list(A=c("A1","A2"),B=c("B1","B2","B3"))
contrast <- "A_vs_B"
norm.data.matrix <- normalize.edaseq(data.matrix,sample.list,gene.data)
p <- stat.bayseq(norm.data.matrix,sample.list,contrast)