Convenience for creating an
SRFilter object appropriate
for ChIP-seq data. Typically, the result is passed
readAligned when loading reads.
A regular expression for excluding chromosomes by name. Just
like the parameter to
The criteria used to determine whether a read is unique. A read may
be unique if it maps to a unique
Whether to require that the read is mapped to a strand, which usually translates to whether the read was mapped at all.
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sp <- SolexaPath(system.file("extdata", package="ShortRead")) filter <- chipseqFilter() aln <- readAligned(sp, "s_2_export.txt", filter=filter) ## allow mapping to the same location (but only if sequence is different) filter <- chipseqFilter(uniqueness = "sequence") aln <- readAligned(sp, "s_2_export.txt", filter=filter) ## allow sex chromosomes filter <- chipseqFilter(exclude = "[M_]") aln <- readAligned(sp, "s_2_export.txt", filter=filter)
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