Shape-class: Class 'Shape' for Shape Feature Coefficients

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

Description

Defines an S4 class to represent shape feature coefficients.

Slots

seedLen

number of base pairs in the seeding model.

Shape.upFootprintExtend

number of upstream positions to fit shape features beyond the seed.

Shape.downFootprintExtend

number of downstream positions to fit shape features 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.

Shape.set

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

Shape.equivMat

matrix encoding reverse complement symmetries between positions with -1 at Shape.equivMat[position1, position2] entry. All other entries are 0.

Shape.values

beta values for positions in Shape.set.

Shape.errors

beta value errors for positions in Shape.set.

Shape.z

beta value z scores for positions in Shape.set.

Shape.sig

beta value significance for positions in Shape.set.

Shape.oldValues

previous iteration beta values for positions in Shape.set.

Shape.oldErrors

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

Shape.oldZ

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

Shape.oldSig

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

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