selex.fastqPSFM {SELEX} | R Documentation |
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.
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.
# 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)))