demultiplexReads: Performs MID/Multiplex filtering

In R453Plus1Toolbox: A package for importing and analyzing data from Roche's Genome Sequencer System

Description

Roche's Genome Sequencer allows to load two or more samples on one region. To allocate sequences to samples, each sample has a unique multiplex sequence. The multiplex sequence should be the prefix of all sequences from that sample. This method demultiplexes a given set of sequences according to the given multiplex sequences (MIDs).

Usage

## S4 method for signature 'XStringSet,XStringSet,numeric,logical'
demultiplexReads(reads, mids, numMismatches, trim)

Arguments

reads	A DNAStringSet instance that contains reads starting with MIDs
mids	A DNAStringSet instance that contains the MIDs
numMismatches	The maximal number of mismatches allowed, default 2.
trim	Whether the MIDs should be cutted-out, default TRUE

Details

All given MIDs must have the same length. The algorithm computes the number of mismachtes for each MID. The read is assigned to the MID with the lowest number of mismatches. If two or more MIDs have the same number of mismachtes, or if the number of mismachtes is greater than the given argument numMismachtes, the read is not assigned to any MID. The default number of allowed mismatches is 2.

Value

demultiplexReads returns a list with one DNAStringSet instance for each MID.

Author(s)

Hans-Ulrich Klein

See Also

genomeSequencerMIDs, DNAStringSet

Examples

	library(Biostrings)
    mids = genomeSequencerMIDs(c("MID1", "MID2", "MID3"))
    reads = DNAStringSet(c(
        paste(as.character(mids[["MID1"]]), "A", sep=""),
        paste(as.character(mids[["MID1"]]), "AA", sep=""),
        paste(as.character(mids[["MID2"]]), "AAA", sep="")))
    demultiplexReads(reads, mids)

R453Plus1Toolbox documentation built on Nov. 8, 2020, 5:59 p.m.