deseqInterest {IntEREst} | R Documentation |
Differential intron retention test adapted from the DESeq2
package.
deseqInterest (x, design, pAdjustMethod = "BH", sizeFactor=c(), contrast, bpparam, ...)
x |
Object of type |
design |
Formula specifying the design of the experiment. It must specify an interaction
term between variables from column names of |
pAdjustMethod |
What adjustment method to be sed on the p-values. See p.adjust for more information. |
sizeFactor |
Numeric vector with the same size as the clolumn size of the count matrix in
|
contrast |
Argument speciftying the comparison to extract from |
bpparam |
An optional |
... |
Other parameter settings for the results function
in the |
a DESeqResults
object.
Ali Oghabian
exactTestInterest
qlfInterest
,
treatInterest
DEXSeqIntEREst
mdsChr22IntObj<- mdsChr22Obj[rowData(mdsChr22Obj)$int_ex=="intron",] deseqRes<- deseqInterest(x=mdsChr22IntObj, design=~test_ctrl, contrast=list("test_ctrl_test_vs_ctrl")) # Number of U12/U2 type significantly differential retained introns in chr22 table(rowData(mdsChr22Obj)[which(deseqRes$padj<.01), "intron_type"])