vmatchPattern2: String searching function.

In vroh/BC32_BarSeq: Set of functions to process and analyze a BC32 sequencing run

Description

A functions for finding all the occurrences (aka "matches" or "hits") of a given pattern (typically short) in a (typically long) reference sequence or set of reference sequences (aka the subject). This is an updated version of vmatchPattern that take indels into account. Provided by Hervé Pagès on https://support.bioconductor.org/p/58350/

Usage

vmatchPattern2(
  pattern,
  subject,
  max.mismatch = 0,
  min.mismatch = 0,
  with.indels = FALSE,
  fixed = TRUE,
  algorithm = "auto"
)

Arguments

pattern	The pattern string.
subject	The String object for matching.
max.mismatch, min.mismatch	The minimum and maximum number of mismatching letters allowed.
with.indels	If TRUE then indels are allowed.
fixed	If TRUE (the default), an IUPAC ambiguity code in the pattern can only match the same code in the subject, and vice versa.
algorithm	One of the following: "auto", "naive-exact", "naive-inexact", "boyer-moore", "shift-or" or "indels".
...	Additional arguments for methods.

Details

See vmatchPattern for details.

Examples

x <- DNAString("AAGCGCGATATG")
m1 <- matchPattern("GCNNNAT", x)
m1

vroh/BC32_BarSeq documentation built on Jan. 25, 2021, 9:24 p.m.