addGeneAligns {spliceSites} | R Documentation |
bamReader
,
refGenome
and gene name.Locates gene in genome via refGenome
and reads a
bamRange
from the determined region.
addGeneAligns(x)
x |
gapSites. The result contains a copy of the passed object. |
The function adds a gene_aligns
column
to the contained data.frame
.
gapSites
Wolfgang Kaisers
# A) Read gapSites bam <- system.file("extdata", "rna_fem.bam", package="spliceSites") reader <- bamReader(bam, idx=TRUE) ga <- alignGapList(reader) bamClose(reader) # B) Annotate ucf <- system.file("extdata", "uc_small_junc.RData", package="spliceSites") ucj <- loadGenome(ucf) annotation(ga) <- annotate(ga, ucj) # C) align part gal <- addGeneAligns(ga) gal