identifySTRRegions,ShortReadQ-method {STRMPS}

Identify the STR regions of a fastq-file or ShortReadQ-object.

Description

identifySTRRegions takes a fastq-file location or a ShortReadQ-object and identifies the STR regions based on a directly adjacent flanking regions. The function allows for mutation in the flanking regions through the numberOfMutation argument.

Usage

## S4 method for signature 'ShortReadQ'
identifySTRRegions(reads, flankingRegions,
  numberOfMutation = 1, control = identifySTRRegions.control())

Arguments

reads

a ShortReadQ-object

flankingRegions

containing marker ID/name, the directly adjacent forward and reverse flanking regions, used for identification.

numberOfMutation

the maximum number of mutations (base-calling errors) allowed during flanking region identification.

control

an identifySTRRegions.control-object.

Value

The returned object is a list of lists. If the reverse complement strings are not included or if the control$combineLists == TRUE, a list, contains lists of untrimmed and trimmed strings for each row in flankingRegions. If control$combineLists == FALSE, the function returns a list of two such lists, one for forward strings and one for the reverse complement strings.

Examples

library("Biostrings")
library("ShortRead")

# Path to file
readPath <- system.file('extdata', "sampleSequences.fastq", package = 'STRMPS')

# Flanking regions
data("flankingRegions")

# Read the file into memory
readFile <- readFastq(readPath)
sread(readFile)
quality(readFile)

# Identify the STR's of the file, both readPath and readFile can be used.

identifySTRRegions(reads = readFile, flankingRegions = flankingRegions,
                   numberOfMutation = 1,
                   control = identifySTRRegions.control(
                       numberOfThreads = 1,
                       includeReverseComplement = FALSE)
                   )