N-class: Class 'N' for Mononucleotide Features

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

Description

Defines an S4 class to represent mononuclueotide features.

Slots

seedLen

number of base pairs in the seeding model.

N.upFootprintExtend

number of upstream nucleotides to fit beyond the seed.

N.downFootprintExtend

number of downstream nucleotides to fit beyond the seed.

fS.upFootprintExtend

maximum number of upstream positions to be fit beyond the footprint for any feature.

fS.downFootprintExtend

maximum number of downstream positions to be fit beyond the footprint for any feature.

fpLen

footprint length for full set of features.

N.set

set of positions for which mononucleotides are fit where positions are given relative to the full feature set footprint.

N.equivMat

matrix encoding reverse complement symmetries between positions with -1 and identical beta values shared between positions with 1.

N.values

beta values for positions in N.set.

N.errors

beta value errors for positions in N.set.

N.z

beta value z scores for positions in N.set.

N.sig

beta value significance for positions in N.set.

N.oldValues

previous iteration beta values for positions in N.set.

N.oldErrors

previous iteration beta values' errors for positions in N.set.

N.oldZ

previous iteration beta values' z scores for positions in N.set.

N.oldSig

previous iteration beta values' significance for positions in N.set.

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