spliceGene: Calculate Splicing Scores for One Gene

In yuhuihui2011/vasp_test: Quantification and Visulization of Variations of Splicing in Population

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)]

yuhuihui2011/vasp_test documentation built on March 5, 2020, 12:50 a.m.