spliceGenome {vasp} | R Documentation

## Calculate Genome-wide Splicing Scores

### Description

Calculate splicing scores from ballgown objects for all genes.

### Usage

    spliceGenome(bg, gene.select = "rowQuantiles(x,probs = 0.05)>=1",
        intron.select = "rowQuantiles(x,probs = 0.95)>=5")

### Arguments

`bg` | ballgown object
`gene.select` | logical expression-like string, indicating genes to select from a matrix of gene-level coverages: NA value keeps all genes. e.g. gene.select = 'rowQuantiles(x,probs = 0.05)>=1' keeps the genes with the read coverage greater than or equal to 1 in at least 95 (0.05 quantile). Used to filter low expressed genes.
`intron.select` | logical expression-like string, indicating introns to select from a matrix of junction counts: NA value keeps all introns. e.g. intron.select = 'rowQuantiles(x,probs = 0.95)>=5' keeps the introns with the read count greater than or euqal to 5 in at least 5 (0.95 quantile). Used to filter introns with very few junction reads supporting.

### Details

score = junction count/gene-level per base read coverage. Row functions for matrices in `matrixStats` package are useful to select genes and introns.

### Value

a list of two elelments: 'score' is matrix of intron splicing scores with intron rows and sample columns and 'intron' is a `GRanges` object of intron structure. See `structure` in ballgown package

### See Also

`spliceGene`, which calculates splicing scores in one gene.

### Examples

    data(rice.bg)
    rice.bg

    splice<-spliceGenome(rice.bg,gene.select=NA,intron.select=NA)
    names(splice)

    head(splice$score)
    splice$intron

[Package vasp version 0.99.26 Index]