psi {IntEREst} | R Documentation

## Psi values estimation

### Description

Calculating Psi values (percentage spliced in) base on two count matrices from a single or two separate objects.

### 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)

[Package IntEREst version 1.6.2 Index]