stat.bayseq {metaseqR} | R Documentation |
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.
stat.bayseq(object, sample.list, contrast.list = NULL, stat.args = NULL, libsize.list = NULL)
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 |
stat.args |
a list of edgeR statistical algorithm
parameters. See the result of
|
libsize.list |
an optional named list where names
represent samples (MUST be the same as the samples in
|
A named list of the value 1-likelihood that a gene is differentially expressed, whose names are the names of the contrasts.
Panagiotis Moulos
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)