DEXSeqIntEREst: DEXSeq test for IntEREst object

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

View source: R/DEXSeqInterest.R

Description

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

Usage

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

Arguments

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.

Details

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.

Value

A DEXSeqResults object.

Author(s)

Ali Oghabian

See Also

exactTestInterest

Examples

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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)

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