subInterestResult {IntEREst} | R Documentation

## Extract subset of object

### Description

Build a new object using subset of data in an `SummarizedExperiment` object.

### Usage

    subInterestResult(x, selectRow, selectCol,
    	sampleAnnoCol, sampleAnnotation=c())

### Arguments

`x` | Object of type `SummarizedExperiment`.
`selectRow` | Numeric or TRUE/FALSE Vector indicating what rows to extract.
`selectCol` | A vector with Numeric values, character strings (sample names) or TRUE/FALSE Vector indicating what columns to extract.
`sampleAnnoCol` | Which colummn of `colData` of object `x` to consider for subset data extraction.
`sampleAnnotation` | Vector including the annotations to consider for subset data extraction. They should be present in the `sampleAnnoCol` column of the `colData` of `x`.

### Value

An object of calss `SummarizedExperiment`.

### Author(s)

Ali Oghabian

### See Also

`interest`, `InterestResult`.

### Examples

    geneId<- paste("gene", c(rep(1,7), rep(2,7), rep(3,7), rep(4,7)),
    	sep="_")
    readCnt1<- sample(1:100, 28)
    readCnt2<- sample(1:100, 28)
    readCnt3<- sample(1:100, 28)
    readCnt4<- sample(1:100, 28)
    fpkm1<- readCnt1/(tapply(readCnt1, geneId, sum))[geneId]
    fpkm2<- readCnt2/(tapply(readCnt2, geneId, sum))[geneId]
    fpkm3<- readCnt3/(tapply(readCnt3, geneId, sum))[geneId]
    fpkm4<- readCnt4/(tapply(readCnt4, geneId, sum))[geneId]

    # Creating object using test data
    interestDat<-data.frame(
    		int_ex=rep(c(rep(c("exon","intron"),3),"exon"),4),
    		int_ex_num= rep(c(1,1,2,2,3,3,4),4),
    		int_type=rep(c(NA,"U2",NA,"U12",NA,"U2",NA),4),
    		strand=rep("*",28),
    		gene_id= geneId,
    		sam1_readCnt=readCnt1,
    		sam2_readCnt=readCnt2,
    		sam3_readCnt=readCnt3,
    		sam4_readCnt=readCnt4,
    		sam1_fpkm=fpkm1,
    		sam2_fpkm=fpkm2,
    		sam3_fpkm=fpkm3,
    		sam4_fpkm=fpkm4
    )
    readFreqColIndex<- grep("_readCnt$",colnames(interestDat))
    scaledRetentionColIndex<- grep("_fpkm$",colnames(interestDat))
    samNames<-paste("sam", 1:4, sep="")
    frqTmp<-as.matrix(interestDat[, readFreqColIndex])
    sclTmp<-as.matrix(interestDat[, scaledRetentionColIndex])
    colnames(frqTmp)<- samNames
    colnames(sclTmp)<- samNames
    interestResObj<- InterestResult(
    	resultFiles=paste("file",1:4, sep="_"),
    	rowData= interestDat[, -c(readFreqColIndex,
    		scaledRetentionColIndex)],
    	counts= frqTmp,
    	scaledRetention= sclTmp ,
    	scaleLength=TRUE,
    	scaleFragment=FALSE,
    	sampleAnnotation=data.frame(
    		sampleName=paste("sam",1:4, sep=""),
    		gender=c("M","M","F","F"),
    		health=c("healthy","unhealthy","healthy","unhealthy"),
    		row.names=samNames
    	)
    )

    #Build new object
    newObj<- subInterestResult(interestResObj, selectRow=1:20)

    #View newObj
    print(newObj)

[Package IntEREst version 1.4.1 Index]