quantifySplicing {psichomics} | R Documentation |
Quantify alternative splicing events
quantifySplicing(annotation, junctionQuant, eventType = c("SE", "MXE", "ALE", "AFE", "A3SS", "A5SS"), minReads = 10, genes = NULL)
annotation |
List of data frames: annotation for each alternative splicing event type |
junctionQuant |
Data frame: junction quantification |
eventType |
Character: splicing event types to quantify |
minReads |
Integer: discard alternative splicing quantified using a number of reads below this threshold |
genes |
Character: gene symbols for which the splicing quantification of associated splicing events is performed (by default, all splicing events undergo splicing quantification) |
Data frame with the quantification of the alternative splicing events
# Calculate PSI for skipped exon (SE) and mutually exclusive (MXE) events annot <- readFile("ex_splicing_annotation.RDS") junctionQuant <- readFile("ex_junctionQuant.RDS") psi <- quantifySplicing(annot, junctionQuant, eventType=c("SE", "MXE"))