DEXSeqIntEREst: DEXSeq test for IntEREst object
In IntEREst: Intron-Exon Retention Estimator

Description Usage Arguments Details Value Author(s) See Also Examples

Genewise differential exon usage or intron retention test adapted from the DEXSeq package.

1 2	DEXSeqIntEREst (x, design, reducedModel = ~ sample + intex, fitExpToVar, intExCol, geneIdCol, bpparam, silent=TRUE,...)

`x`	Object of type `SummarizedExperiment`.
`design`	Formula specifying the design of the experiment. It must specify an interaction term between a variable from columns of `sampleData(x)` with one of the 'exon', 'intron' or 'intex' (i.e. intron and exon) variables; based on which of these variables are used (exon, intron , or 'intex') the x will be filtered reletively to include exons, introns , or introns and exons. See `DEXSeqDataSet` for more information.
`reducedModel`	The null model formula. By default it is '~ sample + intex'.
`fitExpToVar`	A variable name contained in the column data (i.e. column names of `colData(x)`). See `DEXSeq` for more information.
`intExCol`	Column name (or number) that represents whether each row is "intron" or "exon" in `rowData` of `x`.
`geneIdCol`	Column name (or number of column) in `rowData` of `x`, i.e. `SummarizedExperiment` object, that represents the gene ID of the introns and exons in `x`.
`bpparam`	An optional `BiocParallelParam` instance defining the parallel back-end to be used.
`silent`	Whether run the DEXSeq function silently (if TRUE) or allow it to print messages at each step (if FALSE).
`...`	Other parameter settings for the `DEXSeqDataSet` function in the `DEXSeq` package.

The design and reduceModel accept formula that specify the design of the experiment. The formula must describe an interaction between variables from columns of sampleData(x) with one of the 'exon', 'intron' or 'intex' (i.e. intron and exon) variables; Based on which of these variables are used (exon, intron , or 'intex') the input object (x) will be filtered reletively to include exons, introns , or introns and exons. Hence the number of the rows of the returned value is equal to the number of the rows of the filtered object, i.e. the number of the exons, introns or both based on the design formula.

A DEXSeqResults object.

Ali Oghabian

exactTestInterest

dexseqExRes<-DEXSeqIntEREst (x=mdsChr22ExObj, 
	design= ~ sample + exon + test_ctrl:exon, 
	reducedModel = ~ sample + exon, fitExpToVar="test_ctrl", 
	intExCol="int_ex", geneIdCol="transcripts_id", silent=TRUE)
head(dexseqExRes)