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

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

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 'extractedReadsListReverseComplement'
stringCoverage(extractedReadsListObject,
  control = stringCoverage.control())

Arguments

extractedReadsListObject	an extractedReadsList-object, created using the identifySTRRegions-function.
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")

# Limiting and restructuring
sortedIncludedMarkers <- sapply(names(identifiedSTRs$identifiedMarkersSequencesUniquelyAssigned),
                                function(m) which(m == flankingRegions$Marker))

# Aggregate the strings
stringCoverage(extractedReadsListObject = identifiedSTRs,
               control = stringCoverage.control(
                   motifLength = flankingRegions$MotifLength[sortedIncludedMarkers],
                   Type = flankingRegions$Type[sortedIncludedMarkers],
                   numberOfThreads = 1,
                   trace = FALSE,
                   simpleReturn = TRUE))

svilsen/STRMPS documentation built on May 31, 2019, 7:55 a.m.