ShortRead-deprecated: Deprecated functions from the ShortRead package
In ShortRead: FASTQ input and manipulation

These functions are deprecated, and will become defunct.

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

`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.

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

ShortRead documentation built on Nov. 8, 2020, 8:02 p.m.