interestResult: Building SummarizedExperiment object from results in...

InterestResultR Documentation

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 July 29, 2024, 1:12 a.m.