selex.samplePSFM {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 a sample, regardless of sequence filtering.

### Usage

    selex.samplePSFM(sample)

### Arguments

`sample` | A sample handle to the dataset on which the PSFM is calculated.

### Details

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

### Value

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

### See Also

`selex.kmerPSFM`

### Examples

    # Display all currently loaded samples
    selex.sampleSummary()

    r0 = selex.sample(seqName="R0.libraries", sampleName="R0.barcodeGC", round=0)

    # Make PSFMs for the two visible FASTQ files:
    psfm1 = selex.samplePSFM(r0)

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

[Package SELEX version 1.12.0 Index]