This function is a wrapper over DESeq statistical testing. It accepts a matrix of normalized gene counts or an S4 object specific to each normalization algorithm supported by metaseqR2.
a matrix or an object specific to each normalization algorithm supported by metaseqR2, containing normalized counts. See also Details.
the list containing condition names and the samples under each condition.
vector of contrasts as defined in the
main help page of
a list of DESeq statistical algorithm
parameters. See the result of
object, apart from
for NOISeq), the object can be a
contrastList it can also be a named
structured list of contrasts as returned by the internal
A named list of p-values, whose names are the names of the contrasts.
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dataMatrix <- metaseqR2:::exampleCountData(1000) sampleList <- list(A=c("A1","A2"),B=c("B1","B2","B3")) contrast <- "A_vs_B" normDataMatrix <- metaseqR2:::newCountDataSet(dataMatrix, c("A","A","B","B","B")) normDataMatrix <- normalizeDeseq(dataMatrix,sampleList) p <- statDeseq(normDataMatrix,sampleList,contrast)
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