STRMPS (version 0.6.8)

stringCoverage,extractedReadsListCombined-method: 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 extractedReadsListCombined
stringCoverage(
  extractedReadsListObject,
  flankingRegions,
  control = stringCoverage.control()
)

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.

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.

Examples

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

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