deseqInterest: DESeq2 analysis for IntEREst object

In IntEREst: Intron-Exon Retention Estimator

Description

Differential intron retention test adapted from the DESeq2 package.

Usage

deseqInterest (x, design, pAdjustMethod = "BH", 
	sizeFactor=c(), contrast, bpparam, ...)

Arguments

x	Object of type SummarizedExperiment.
design	Formula specifying the design of the experiment. It must specify an interaction term between variables from column names of sampleData(x).
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 x, if defined it will be used for scaling of the count matrix.
contrast	Argument speciftying the comparison to extract from x. See results function in the DESeq2 package for more information.
bpparam	An optional BiocParallelParam instance defining the parallel back-end to be used. If not defined the function will run sequentially (on a single computing core).
...	Other parameter settings for the results function in the DESeq2 package.

Value

a DESeqResults object.

Author(s)

Ali Oghabian

See Also

exactTestInterest qlfInterest, treatInterest DEXSeqIntEREst

Examples

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"])

IntEREst documentation built on Nov. 8, 2020, 8:05 p.m.