## discovery
renewable()
renewable("AlignedRead")
renewable("QualityScore") ## instantiable classes
## example data
sp <- SolexaPath(system.file("extdata", package="ShortRead"))
ap <- analysisPath(sp)
filt <- chromosomeFilter("chr[[:digit:]+].fa")
aln <- readAligned(ap, "s_2_export.txt", "SolexaExport",
filter=filt)
## renew chromosomes from 'chr1.fa' to 'chr1', etc
labels <- sub("\\.fa", "", levels(chromosome(aln)))
renew(aln, chromosome=factor(chromosome(aln), labels=labels))
## multiple changes -- update chromosome, offset position
renew(aln, chromosome=factor(chromosome(aln), labels=labels),
position=1L+position(aln))
## oops! invalid instances cannot be constructed
try(renew(aln, position=1:10))
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