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.

### References

Yu, H., Du, Q., Campbell, M., Yu, B., Walia, H. and Zhang, C. (2021), Genome‐wide discovery of natural variation in pre‐mRNA splicing and prioritising causal alternative splicing to salt stress response in rice. New Phytol. https://doi.org/10.1111/nph.17189

### 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 1.4.0 Index]