spliceGenome {vasp} | R Documentation |
Calculate splicing scores from ballgown objects for all genes.
spliceGenome(bg, gene.select = "rowQuantiles(x,probs = 0.05)>=1", intron.select = "rowQuantiles(x,probs = 0.95)>=5")
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. |
score = junction count/gene-level per base read coverage.
Row functions for matrices in matrixStats
package are useful
to select genes and introns.
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
spliceGene
, which calculates splicing scores in one
gene.
data(rice.bg) rice.bg splice<-spliceGenome(rice.bg,gene.select=NA,intron.select=NA) names(splice) head(splice$score) splice$intron