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

### 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 Prioritizing Causal Alternative Splicing to Salt Stress Response in Rice. New Phytol. https://doi.org/10.1111/nph.17189

### 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 1.2.4 Index]