spliceGenome: Calculate Genome-wide Splicing Scores

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

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

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