interestResult: Building SummarizedExperiment object from results in...

In gacatag/IntEREst: Intron-Exon Retention Estimator

Building SummarizedExperiment object from results in IntEREst.

Description

Calls the constructors and creates a SummarizedExperiment object. For more information on the resulted object and the class see SummarizedExperiment-class.

Usage

InterestResult(resultFiles=c(), counts, scaledRetention, 
	scaleLength, scaleFragment, sampleAnnotation, rowData)

Arguments

resultFiles	Vector of link to the result files of interest.
counts	Numeric Matrix that includes the read counts.
scaledRetention	Matrix that includes the scaled retention values.
scaleLength	Logical value, indicating whether the intron/exon retention levels are scaled to the length of the introns/exons.
scaleFragment	Logical value, indicating whether the intron/exon retention levels are scaled to the fragments mapped to the genes.
sampleAnnotation	Data frame with the row-size equal to the size of resultFiles and sampleAnnotation. Each column of the matrix represents annotations for the samples. Column name represents annotation name.
rowData	Data frame with Intron/Exon annotations and read count and scaled retention values for each sample.

Value

Returns an object of class SummarizedExperiment.

Author(s)

Ali Oghabian

See Also

SummarizedExperiment-class attributes addAnnotation counts-method plot-method

Examples

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"), row.names=paste("sam", 1:4, sep="")
	)
)

# View object
InterestResultObj

gacatag/IntEREst documentation built on Aug. 20, 2023, 6:06 p.m.