counts-method {IntEREst} | R Documentation

## Counts - method

### Description

Returns the (row) number of reads that are mapped to introns/exons in various samples.

### Usage

    ## S4 method for signature 'SummarizedExperiment'
    counts(object)

### Arguments

`object` | Object of type `SummarizedExperiment`.

### Value

Returns a numeric matrix.

### Author(s)

Ali Oghabian

### See Also

Class: `SummarizedExperiment-class`

Method: `plot-method`.

### Examples

    #Show contents of a InterestResults object included in IntEREst
    head(counts(mdsChr22Obj))

    #Make a test InterestResults object
    geneId<- paste("gene", c(rep(1,5), rep(2,5), rep(3,5), rep(4,5)),
    	sep="_")
    readCnt1<- sample(1:100, 20)
    readCnt2<- sample(1:100, 20)
    readCnt3<- sample(1:100, 20)
    readCnt4<- sample(1:100, 20)
    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"),2),"exon"),4),
    		int_ex_num= rep(c(1,1,2,2,3),4),
    		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))

    scalRetTmp<- as.matrix(interestDat[ ,scaledRetentionColIndex])
    colnames(scalRetTmp)<-gsub("_fpkm$","", colnames(scalRetTmp))

    frqTmp<- as.matrix(interestDat[ ,readFreqColIndex])
    colnames(frqTmp)<-gsub("_readCnt$","", colnames(frqTmp))

    InterestResultObj<- InterestResult(
    	resultFiles=paste("file",1:4, sep="_"),
    	rowData= interestDat[ , -c(readFreqColIndex,
    		scaledRetentionColIndex)],
    	counts= frqTmp,
    	scaledRetention= scalRetTmp,
    	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=paste("sam", 1:4, sep="")
    	)
    )

    #Show
    head(counts(InterestResultObj))

[Package IntEREst version 1.4.1 Index]