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

In IntEREst: Intron-Exon Retention Estimator

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

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

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 Nov. 8, 2020, 8:05 p.m.