subInterestResult: Extract subset of object

In IntEREst: Intron-Exon Retention Estimator

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)

IntEREst documentation built on Nov. 8, 2020, 8:05 p.m.