getKmerCountAffinities: Create k-mer affinity table for seeding GLM analysis of SELEX...

In BussemakerLab/SelexGLM: Functions for performing feature-based analyis of SELEX-seq data using generalized linear models

Description

Create k-mer affinity table for seeding GLM analysis of SELEX data.

Usage

getKmerCountAffinities(sample, k, markovModel, minCount = 100,
  symmetrize = TRUE)

Arguments

k	K-mer length to be counted.
markovModel	Markov model handle to use to predict previous round probabilities and expected counts.
minCount	The minimum number of counts for a k-mer to be output.
symmetrize	logical: indicates whether count cutoff and sorting should be imposed on the symmetrized counts/affinities.
Sample	Sample handle to the dataset on which k-mer counting should be perfomed.

Value

A data frame containing k-mer affinities (standard and reverse complement symmetric versions).

BussemakerLab/SelexGLM documentation built on May 17, 2019, 5:41 p.m.