ShortRead-deprecated {ShortRead} | R Documentation

## 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

[Package ShortRead version 1.38.0 Index]