psi: Psi values estimation

In IntEREst: Intron-Exon Retention Estimator

Description

Calculating the relative inclusion level of intron or Psi values base on two count matrices from a single or two separate objects. The values for each intron is in the range of [0,1], where 0 means complete splicing or no retention of the intron and 1 represnet complete 100

Usage

psi (x, y, intCol, exCol, pseudoCnt=0)

Arguments

x	Object of type SummarizedExperiment.
y	Optional; i.e. an object of type SummarizedExperiment.
intCol	Column numbers or column names in counts matrix of x which include the number of reads mapped to the introns.
exCol	Column numbers or column names in counts matrix of x (or if defined y) which include the number of reads spanning the introns (or mapping exons flanking the introns).
pseudoCnt	Pseudo counts to sum to the denominator of the devision to avoid devision to zero.

Value

data.frame with column size equal to the size of intCol parameter, and row size equal to the number of rows in x. It contains the psi values (i,e.values between 0 and 1 showing the fraction of spliced in transcripts).

Author(s)

Ali Oghabian

See Also

interestResultIntEx

Examples

mdsChr22IntObj<- mdsChr22Obj[which(rowData(mdsChr22Obj)$int_ex=="intron"), ]

#Build object including intron-retention and exon-junction results
mdsChr22RefIntExObj<- interestResultIntEx(intObj=mdsChr22Obj, 
	exObj=mdsChr22ExObj, mean.na.rm=TRUE, postExName="ex_junc", 
	intExCol="int_ex" )
# Calculate Psi
psiRes<- psi(mdsChr22RefIntExObj,
	intCol=which(colData(mdsChr22RefIntExObj)$intronExon=="intron"),
	exCol=which(colData(mdsChr22RefIntExObj)$intronExon=="exon"))
# show Psi results
head(psiRes)

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