spliceGene {vasp}R Documentation

Calculate Splicing Scores for One Gene

Description

Calculate splicing Scores from ballgown object for a given gene. This function can only calculate one gene. Please use function spliceGenome to obtain genome-wide splicing scores.

Usage

spliceGene(bg, gene, samples = sampleNames(bg),junc.type = c("score", "count"), 
    trans.select = "rowMaxs(x)>=1", junc.select = "rowMaxs(x)>=5")

Arguments

bg

ballgown object

gene

a character string specifying gene id

samples

names of samples

junc.type

type of junction estimate ('score' for junction score; 'count' for junction read count)

trans.select

logical expression-like string, indicating transcript rows to select from a matrix of transcript coverages: NA value keeps all transcripts. e.g. use trans.select='rowMaxs(x)>=1' to filter the transcrpts with the maximium coverage among all the samples less than 1.

junc.select

logical expression-like string, indicating junction rows to select from a matrix of junction counts: NA value keeps all junctions. e.g. use junc.select='rowMaxs(x)>=5' to filter the junctions with the maximium read count among all the samples less than 5.

Details

score = junction count/gene-level per base read coverage. Row functions for matrices are useful to select transcripts and junctions. See matrixStats package.

Value

a matrix of junction scores with intron rows and sample columns.

See Also

spliceGenome, which calculates splicing scores in whole genome.

Examples

data(rice.bg)
rice.bg
head(geneIDs(rice.bg))

score<-spliceGene(rice.bg,'MSTRG.183',junc.type='score')
count<-spliceGene(rice.bg,'MSTRG.183',junc.type='count')

## compare
tail(score)
tail(count)

## get intron structrue
intron<-structure(rice.bg)$intron
intron[intron$id%in%rownames(score)]

[Package vasp version 1.0.0 Index]