demultiplexReads {R453Plus1Toolbox} | R Documentation

## Performs MID/Multiplex filtering

### 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)

[Package R453Plus1Toolbox version 1.40.0 Index]