createPWM: Create position weight matrix from multiple sequence...

Description Usage Arguments Details Value Examples

Description

Create position weight matrix from multiple sequence alignment

Usage

1

Arguments

msa

A DNAStringSet object of aligned sequences.

indelRate

<numeric|NULL>; The estimated background rate of Indels.

Details

PWM: a matrix with position as row names and nucleotides as column manes. Values are nucleotide weights at a position A ConsensusMatrix is calculated from the MSA using Biostrings::consensusMatrix and values are converted to probabilities. Pseudocounts are added and values are divided by DNA probabilities and log2 score is reported

Value

A PWM matrix.

Examples

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2
print("TODO: Add examples")
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gschofl/DR2S documentation built on May 17, 2019, 8:40 a.m.