spliceGene {vasp} | R Documentation |
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.
spliceGene(bg, gene, samples = sampleNames(bg),junc.type = c("score", "count"), trans.select = "rowMaxs(x)>=1", junc.select = "rowMaxs(x)>=5")
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. |
score = junction count/gene-level per base read coverage.
Row functions for matrices are useful to select transcripts and junctions.
See matrixStats
package.
a matrix of junction scores with intron rows and sample columns.
spliceGenome
, which calculates splicing scores in
whole genome.
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)]