inst/examples/identify.R

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

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.
\donttest{
identifySTRRegions(reads = readFile, flankingRegions = flankingRegions,
                   numberOfMutation = 1,
                   control = identifySTRRegions.control(
                       numberOfThreads = 1,
                       includeReverseComplement = FALSE)
                   )
}