interestResultIntEx: Building results object that contains Intron-retention and...

Description Usage Arguments Value Author(s) See Also Examples

View source: R/interestResultIntEx.R

Description

Building SummarizedExperiment-class object from an intron retention and an exon-exon junction results in IntEREst. The average of the junction levels are added to the SummerizedExperiment object of the intron retentions.

Usage

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interestResultIntEx (intObj, exObj, intExCol=c(), 
	mean.na.rm=TRUE, postExName="ex_junc" )

Arguments

intObj

A SummarizedExperiment including intron retention information.

exObj

A SummarizedExperiment including exon-exon junction information.

intExCol

Column name (or number) in the rowData of the intron object that represents whether each row of x assays is "intron" or "exon".

mean.na.rm

Whether exclude missing values when measuring the mean.

postExName

The postfix to use for the column names of the exons junction values in the

Value

Returns an object of class SummarizedExperiment.

Author(s)

Ali Oghabian

See Also

SummarizedExperiment-class attributes addAnnotation counts-method plot-method

Examples

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testIntObj<- InterestResult(
		resultFiles= paste(paste("testFile",1:3, sep="_"),"bam", sep="."), 
		counts= matrix(1:15, ncol=3, nrow=5, byrow=TRUE, 
			dimnames= list(c(), paste("s", 1:3, sep="_"))), 
		scaledRetention= matrix(1:15, ncol=3, nrow=5, byrow=TRUE, 
			dimnames= list(c(), paste("s", 1:3, sep="_"))), 
		scaleLength= FALSE, 
		scaleFragment= FALSE, 
		sampleAnnotation= data.frame(
			files=paste(paste("testFile",1:3, sep="_"),"bam", sep="."),
			names=paste("s", 1:3, sep="_"),
			row.names=paste("s", 1:3, sep="_")), 
		rowData=data.frame(id= paste("i", 1:5, sep="_"),
			chr= rep("chr1", 5),
			begin=seq(100, by=100, length.out=5 ),
			end=seq(110, by=100, length.out=5 ),
			strand=rep("+",5))
	)

testExObj<- InterestResult(
		resultFiles= paste(paste("testFile",1:3, sep="_"),"bam", sep="."), 
		counts= matrix(1:30, ncol=3, nrow=10, byrow=TRUE, 
			dimnames= list(c(), paste("s", 1:3, sep="_"))), 
		scaledRetention= matrix(1:30, ncol=3, nrow=10, byrow=TRUE, 
			dimnames= list(c(), paste("s", 1:3, sep="_"))), 
		scaleLength= FALSE, 
		scaleFragment= FALSE, 
		sampleAnnotation= data.frame(
			files=paste(paste("testFile",1:3, sep="_"),"bam", sep="."),
			names=paste("s", 1:3, sep="_"),
			row.names=paste("s", 1:3, sep="_")), 
		rowData=data.frame(id= paste("e", 1:10, sep="_"),
			chr= rep("chr1", 10),
			begin= c(seq(90, by=100, length.out=5),
				seq(111, by=100, length.out=5)),
			end= c(seq(99, by=100, length.out=5),
				seq(120, by=100, length.out=5 )),
			strand=rep("+",10))
	)


(testIntExObj<- interestResultIntEx(intObj=testIntObj, exObj=testExObj, 
	mean.na.rm=TRUE, postExName="ex_junc" ) )

IntEREst documentation built on May 3, 2018, 6 p.m.