parseMisoEventID {psichomics} | R Documentation

## 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)

[Package psichomics version 1.20.2 Index]