Filtering ChIP-seq reads

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Description

Convenience for creating an SRFilter object appropriate for ChIP-seq data. Typically, the result is passed to readAligned when loading reads.

Usage

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chipseqFilter(exclude = "[_MXY]", uniqueness = c("location", "sequence", "location*sequence", "none"), hasStrand = TRUE)

Arguments

exclude

A regular expression for excluding chromosomes by name. Just like the parameter to bsapply.

uniqueness

The criteria used to determine whether a read is unique. A read may be unique if it maps to a unique location, has a unique sequence or both. Specifying none avoids this test entirely.

hasStrand

Whether to require that the read is mapped to a strand, which usually translates to whether the read was mapped at all.

Value

An SRFilter object

Author(s)

M. Lawrence

Examples

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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)