flagByUpstreamSequences: Filter by upstream sequences

In charles-plessy/CAGEr: Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining

Filter by upstream sequences

Description

Looks up the bases directly upstream provided genomic ranges and searches for a gapless match with a target seqence within a given edit distance.

Usage

flagByUpstreamSequences(object, target, distance = 0)

## S4 method for signature 'CTSS'
flagByUpstreamSequences(object, target, distance = 0)

## S4 method for signature 'TagClusters'
flagByUpstreamSequences(object, target, distance = 0)

## S4 method for signature 'ConsensusClusters'
flagByUpstreamSequences(object, target, distance = 0)

## S4 method for signature 'GRanges'
flagByUpstreamSequences(object, target, distance = 0)

Arguments

object	A CTSS, a TagClusters, ConsensusClusters or a GenomicRanges::GRanges object from which a BSgenome object can be reached.
target	A target sequence.
distance	The maximal edit distance between the genome and the target sequence (default: 0).

Details

If the provided object represents tag clusters or consensus clusters, the search will be done upstream its dominant peak. Convert the object to the GRanges class if this is not the behaviour you want.

Value

A logical-RLe vector indicating if ranges matched the target.

Author(s)

Charles Plessy

See Also

Other CAGEr filter functions: filteredCTSSidx(), flagLowExpCTSS()

charles-plessy/CAGEr documentation built on Oct. 27, 2024, 10:11 p.m.