psi {IntEREst} | R Documentation |
Calculating Psi values (percentage spliced in) base on two count matrices from a single or two separate objects.
psi (x, y, intCol, exCol, pseudoCnt=0)
x |
Object of type |
y |
Optional; i.e. an object of type |
intCol |
Column numbers or column names in counts matrix of |
exCol |
Column numbers or column names in counts matrix of |
pseudoCnt |
Pseudo counts to sum to the denominator of the devision to avoid devision to zero. |
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).
Ali Oghabian
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)