selex.fastqPSFM {SELEX} | R Documentation

## Construct a diagnostic PSFM for a FASTQ file

### Description

A function used to calculate and return the PFSM (Position Specific Frequency Matrix) for an entire FASTQ file, regardless of barcode or other sequence filtering.

### Usage

    selex.fastqPSFM(seqName)

### Arguments

`seqName` | A sequencing run name for the desired FASTQ file; this must match a sequencing run name of a sample currently visible to the SELEX session.

### Details

The output can be used by the `seqLogo` package to create a sequence logo.

### Value

`selex.fastqPSFM` returns a matrix containing the frequences for each base at every position.

### See Also

`selex.kmerPSFM`

### Examples

    # Display all currently loaded samples
    selex.sampleSummary()

    # Make PSFMs for the two visible FASTQ files:
    psfm1 = selex.fastqPSFM(seqName='R0.libraries')
    psfm2 = selex.fastqPSFM(seqName='R2.libraries')

    # Can make sequence logos using the seqLogo package:
    #library(seqLogo)
    #seqLogo(makePWM(t(psfm1)))

[Package SELEX version 1.22.0 Index]