interestResultIntEx {IntEREst} | R Documentation

## Building results object that contains Intron-retention and exon-exon junction information

### 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" ) )

[Package IntEREst version 1.4.1 Index]