statDeseq {metaseqR2} | R Documentation |
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.
statDeseq(object, sampleList, contrastList = NULL, statArgs = NULL)
object |
a matrix or an object specific to each normalization algorithm supported by metaseqR2, containing normalized counts. See also Details. |
sampleList |
the list containing condition names and the samples under each condition. |
contrastList |
vector of contrasts as defined in the
main help page of |
statArgs |
a list of DESeq statistical algorithm
parameters. See the result of
|
Regarding object
, apart from matrix
(also
for NOISeq), the object can be a SeqExpressionSet
(EDASeq), CountDataSet
(DESeq), DGEList
(edgeR), DESeqDataSet
(DESeq2), SeqCountSet
(DSS) or ABSDataSet
(ABSSeq).
Regarding contrastList
it can also be a named
structured list of contrasts as returned by the internal
function metaseqR2:::makeContrastList
.
A named list of p-values, whose names are the names of the contrasts.
Panagiotis Moulos
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)