interestResultIntEx {IntEREst} | R Documentation |
Building SummarizedExperiment-class
object
from an intron retention and an exon-exon junction results in IntEREst. The
average of the junction levels are added to the SummerizedExperiment object of
the intron retentions.
interestResultIntEx (intObj, exObj, intExCol=c(), mean.na.rm=TRUE, postExName="ex_junc" )
intObj |
A |
exObj |
A |
intExCol |
Column name (or number) in the |
mean.na.rm |
Whether exclude missing values when measuring the mean. |
postExName |
The postfix to use for the column names of the exons junction values in the |
Returns an object of class SummarizedExperiment
.
Ali Oghabian
SummarizedExperiment-class
attributes
addAnnotation
counts-method
plot-method
testIntObj<- InterestResult( resultFiles= paste(paste("testFile",1:3, sep="_"),"bam", sep="."), counts= matrix(1:15, ncol=3, nrow=5, byrow=TRUE, dimnames= list(c(), paste("s", 1:3, sep="_"))), scaledRetention= matrix(1:15, ncol=3, nrow=5, byrow=TRUE, dimnames= list(c(), paste("s", 1:3, sep="_"))), scaleLength= FALSE, scaleFragment= FALSE, sampleAnnotation= data.frame( files=paste(paste("testFile",1:3, sep="_"),"bam", sep="."), names=paste("s", 1:3, sep="_"), row.names=paste("s", 1:3, sep="_")), rowData=data.frame(id= paste("i", 1:5, sep="_"), chr= rep("chr1", 5), begin=seq(100, by=100, length.out=5 ), end=seq(110, by=100, length.out=5 ), strand=rep("+",5)) ) testExObj<- InterestResult( resultFiles= paste(paste("testFile",1:3, sep="_"),"bam", sep="."), counts= matrix(1:30, ncol=3, nrow=10, byrow=TRUE, dimnames= list(c(), paste("s", 1:3, sep="_"))), scaledRetention= matrix(1:30, ncol=3, nrow=10, byrow=TRUE, dimnames= list(c(), paste("s", 1:3, sep="_"))), scaleLength= FALSE, scaleFragment= FALSE, sampleAnnotation= data.frame( files=paste(paste("testFile",1:3, sep="_"),"bam", sep="."), names=paste("s", 1:3, sep="_"), row.names=paste("s", 1:3, sep="_")), rowData=data.frame(id= paste("e", 1:10, sep="_"), chr= rep("chr1", 10), begin= c(seq(90, by=100, length.out=5), seq(111, by=100, length.out=5)), end= c(seq(99, by=100, length.out=5), seq(120, by=100, length.out=5 )), strand=rep("+",10)) ) (testIntExObj<- interestResultIntEx(intObj=testIntObj, exObj=testExObj, mean.na.rm=TRUE, postExName="ex_junc" ) )