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

In SELEX: Functions for analyzing SELEX-seq data

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.

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.

Value

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

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)))

SELEX documentation built on Nov. 8, 2020, 5:22 p.m.