stringCoverage-extractedReadsList-method: Get string coverage STR identified objects.

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

Get string coverage STR identified objects.

Description

stringCoverage takes an extractedReadsList-object and finds the coverage of every unique string for every marker in the provided list.

Usage

## S4 method for signature 'extractedReadsList'
stringCoverage(
  extractedReadsListObject,
  flankingRegions,
  control = stringCoverage.control()
)

Arguments

extractedReadsListObject	an extractedReadsList-object, created using the identifySTRRegions-function.
flankingRegions	containing marker ID/name, the directly adjacent forward and reverse flanking regions, used for identification.
control	an stringCoverage.control-object.

Value

Returns a list, with an element for every marker in extractedReadsList-object, each element contains the string coverage of all unique strings of a given marker.

Examples

# Regions identified using 'identifySTRs()'
data("identifiedSTRs")

# Aggregate the strings
stringCoverage(
    extractedReadsListObject = identifiedSTRs,
    flankingRegions = flankingRegions,
    control = stringCoverage.control(
        numberOfThreads = 1,
        trace = FALSE,
        simpleReturn = TRUE
    )
)

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