refFromAlns: refFromAlns

In HLindsay/CrispRVariants: Tools for counting and visualising mutations in a target location

Description

Reconstruct the reference sequence from alignments reads using the CIGAR

Usage

refFromAlns(alns, location, ...)

## S4 method for signature 'GAlignments,ANY'
refFromAlns(alns, location, ...,
  keep.names = FALSE)

## S4 method for signature 'GAlignments,GRanges'
refFromAlns(alns, location, ...)

Arguments

alns	Alignments to use for inferring the reference sequence
location	The location to infer the reference for.
...	additional arguments
keep.names	Should read names be added to the result if present? (Default: FALSE)

Value

The reference sequences corresponding to the provided alignments

A DNAStringSet (signature = c("GAlignments", "ANY"))

A DNAString (signature = c("GAlignments", "GRanges"))

Author(s)

Helen Lindsay

HLindsay/CrispRVariants documentation built on May 28, 2019, 12:40 p.m.