selex.fastqPSFM: Construct a diagnostic PSFM for a FASTQ file
In SELEX: Functions for analyzing SELEX-seq data

Description Usage Arguments Details Value See Also Examples

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.

1	selex.fastqPSFM(seqName)

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.

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

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

selex.kmerPSFM

# 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)))