Description Usage Arguments Details Value Note Author(s) Examples
This function is a wrapper over NBPSeq statistical testing. It accepts a matrix of normalized gene counts or an S4 object specific to each normalization algorithm supported by metaseqR2.
1 2 | statNbpseq(object, sampleList, contrastList = NULL,
statArgs = NULL, libsizeList = 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 NBPSeq statistical algorithm
parameters. See the result of
|
libsizeList |
an optional named list where names
represent samples (MUST be the same as the samples
|
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.
There is currently a problem with the NBPSeq package and the workflow that is specific to the NBPSeq package. The problem has to do with function exporting as there are certain functions which are not recognized from the package internally. For this reason and until it is fixed, only the Smyth workflow will be available with the NBPSeq package.
Panagiotis Moulos
1 2 3 4 5 6 | require(NBPSeq)
dataMatrix <- metaseqR2:::exampleCountData(2000)
sampleList <- list(A=c("A1","A2"),B=c("B1","B2","B3"))
contrast <- "A_vs_B"
normDataMatrix <- normalizeNbpseq(dataMatrix,sampleList)
p <- statNbpseq(normDataMatrix,sampleList,contrast)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.