identifySTRRegions-ShortReadQ-method: Identify the STR regions of a fastq-file or...

In svilsen/STRMPS: Analysis of Short Tandem Repeat (STR) Massively Parallel Sequencing (MPS) Data

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.

svilsen/STRMPS documentation built on Feb. 22, 2025, 4:51 p.m.