twoStepConsensusString: A custom consensus string constructor that uses a two step...

In philliplab/MotifBinner: Bin reads by Motif

Description

First, threshold_1 is applied to search for all positions where a letter occur in that many or more sequences. (threshold_1 must be bigger than 0.5). The letter that occurs at least that frequently will then get put in the consensus sequence.

Usage

twoStepConsensusString(seqs, threshold_1 = 0.501, threshold_2 = 0.25)

Arguments

seqs	The aligned sequences to construct a consensus of
threshold	The percentage of sequences that must have a letter in a certain positon for it to be included in the consensus string

Details

For those positions where there is not a letter that meets threshold_1, threshold_2 will then be used to remove all letters that occur in less than threshold_2 sequences. Using the letters that remain, an ambiguity character will be constructed.

philliplab/MotifBinner documentation built on Sept. 2, 2020, 11:41 a.m.