chipseqFilter {chipseq} | R Documentation |
Convenience for creating an
SRFilter
object appropriate
for ChIP-seq data. Typically, the result is passed
to readAligned
when loading reads.
chipseqFilter(exclude = "[_MXY]", uniqueness = c("location", "sequence", "location*sequence", "none"), hasStrand = TRUE)
exclude |
A regular expression for excluding chromosomes by name. Just
like the parameter to |
uniqueness |
The criteria used to determine whether a read is unique. A read may
be unique if it maps to a unique |
hasStrand |
Whether to require that the read is mapped to a strand, which usually translates to whether the read was mapped at all. |
An SRFilter
object
M. Lawrence
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)