FindSequenceOccurrence: Find occurrences of a DNA sequence in a BSgenome

In ATpoint/dailytRumpet: Unrelated R functions for daily use in bioinformatics that do not fit into any other repository

Description

Function takes a DNA sequence and then returns a GRanges object with the position of that sequence (separated by strand) in a given BSgenome. Optionally one can set a number of allowed mismatches. IUPAC ambiguity characters are supported.

Usage

FindSequenceOccurrence(
  Sequence,
  BSGenome,
  StrictAmbiguity = FALSE,
  MaxMismatches = 0,
  Cores = detectCores()
)

Arguments

Sequence	A DNA sequence
BSGenome	a BSgenome object
StrictAmbiguity	logical, how to deal with ambiguity characters, see Details.
MaxMismatches	number of allowed mismatches
Cores	number of cores for chromosome-wise search parallelization via mclapply

Details

StrictAmbiguity => if TRUE (so strict) then an amb. character in the query, e.g. N is only counted as a match if the reference contains the same character, so N in query must be N in reference. Else, character in reference can be any of the encoded characters, so N can be A/T/C/G in the reference.

Author(s)

Alexander Toenges

Examples

library(BSgenome.Ecoli.NCBI.20080805)
FindSequenceOccurrence(Sequence = "AGCTAAATTTGG", 
                       MaxMismatches = 1,
                       BSGenome = BSgenome.Ecoli.NCBI.20080805)
 

ATpoint/dailytRumpet documentation built on April 28, 2020, 1:47 a.m.