parseMisoEventID: Match MISO's splicing event IDs with the IDs present in the...

In nuno-agostinho/psichomics: Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation

Match MISO's splicing event IDs with the IDs present in the alternative splicing annotation file and get events in a data frame

Description

Match MISO's splicing event IDs with the IDs present in the alternative splicing annotation file and get events in a data frame

Usage

parseMisoEventID(eventID, annotation, IDcolumn)

Arguments

eventID	Character: alternative event IDs
annotation	Data.frame: alternative event annotation file
IDcolumn	Integer: index of the column with the event ID's in the alternative event annotation file

Details

For faster execution times, provide a vector of event IDs.

For more information about MISO, see http://miso.readthedocs.org.

Value

Data frame of the matching events (or NA when nothing matches)

Note

If possible, it's recommend to use smaller subsets of the alternative events' annotation instead of all data for faster runs. For example, when trying to match only skipped exons event IDs, only use the annotation of skipped exons instead of using a mega annotation with all event types.

Examples

eventID <- c("114785@uc001sok.1@uc001soj.1", "114784@uc001bxm.1@uc001bxn.1")
# the annotation is one of the GFF3 files needed to run MISO
gff3 <- system.file("extdata", "miso_AS_annot_example.gff3", 
                    package="psichomics")
annotation <- read.delim(gff3, header=FALSE, comment.char="#")
IDcolumn <- 9
psichomics:::parseMisoEventID(eventID, annotation, IDcolumn)

nuno-agostinho/psichomics documentation built on Jan. 2, 2025, 4:10 a.m.