SELEX (version 1.4.0)

selex.kmerPSFM: Construct a PSFM from a K-mer table

Description

A function used to calculate and return the PFSM (Position Specific Frequency Matrix) for a K-mer table of length k from sample. If an offset value is provided, K-mer counting takes place at a fixed position within the variable region.

Usage

selex.kmerPSFM(sample, k, offset=NULL)

Arguments

sample

A sample handle to the dataset on which K-mer counting should be perfomed.

k

K-mer length(s) to be counted.

offset

Location of window for which K-mers should be counted for. If not provided, K-mers are counted across all windows. offset starts from 0.

Value

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

Details

A K-mer table will be constructed for the specified sample, length k, and offset if it does not already exist.

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

See Also

selex.counts, selex.fastqPSFM

Examples

# Build the PSFM
psfm1 = selex.kmerPSFM(sample=r0, k=8, 0)

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