ShortRead-deprecated: Deprecated functions from the ShortRead package

In Bioconductor/ShortRead: FASTQ input and manipulation

Deprecated functions from the ShortRead package

Description

These functions are deprecated, and will become defunct.

Usage

uniqueFilter(withSread=TRUE, .name="UniqueFilter")

Arguments

withSread	A logical(1) indicating whether uniqueness includes the read sequence (withSread=TRUE) or is based only on chromosome, position, and strand (withSread=FALSE)
.name	An optional character(1) object used to over-ride the name applied to default filters.

Details

See srFilter for details of ShortRead filters.

uniqueFilter selects elements satisfying !srduplicated(x) when withSread=TRUE, and !(duplicated(chromosome(x)) & duplicated(position(x)) & duplicated(strand(x))) when withSread=FALSE.

The behavior when withSread=TRUE can be obtained with occurrenceFilter(withSread=TRUE). The behavior when withSread=FALSE can be obtained using a custom filter

Bioconductor/ShortRead documentation built on Nov. 2, 2024, 4:38 p.m.