selex.samplePSFM: Construct a diagnostic PSFM for a FASTQ file

Description Usage Arguments Details Value See Also Examples

View source: R/SELEX.R

Description

A function used to calculate and return the PFSM (Position Specific Frequency Matrix) for a sample, regardless of sequence filtering.

Usage

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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

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# 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)))

Bioconductor-mirror/SELEX documentation built on June 1, 2017, 1:14 a.m.