model-class: Class model for SelexGLM

Description Slots

Description

An S4 class to represent model object to store library design, model design, and model parameters for a SelexGLM project.

Slots

name

Name to be associated with the model object. If unspecified, empty string is assigned by default.

varRegLen

Length of the library design for the selex data.

leftFixedSeq

Fixed sequence to the left of random library in library design.

rightFixedSeq

Fixed sequence to the right of random library in library design.

seedLen

Length of k-mer used to seed the regression. If unspecified, empty numeric value is assigned by default.

consensusSeq

Optional regular expression input specifying consensus sequence to be used to determine the seed sequence for building a PSAM from the k-mer table used to seed the analysis. If "consensusSeq" is input in iupac notation, it is converted to a standard regular expression during initialization of model object.

leftFixedSeqOverlap

Number of bp into the left fixed flank to be considered in analysis. If unspecified, 0 is assigned by default.

rightFixedSeqOverlap

Number of bp into the right fixed flank to be considered in analysis. If unspecified, rightFixedSeqOverlap is set to leftFixedSeqOverlap by default.

affinityType

name of affinity variable in k-mer table to be used in building the seeding PSAM. If no value is specified, affinityType = 'Affinity'.

numViews

number of distinct views of length k contained in each strand. Must be equal to leftFixedSeqOverlap+varRegLen+rightFixedSeqOverlap.

rounds

list of length 1 with rounds[[1]] equal to a vector containing the rounds of data to be fit.

confidenceLevel

view confidence level cutoff required for probes used in glm fit.

minAffinity

minimum view affinity required for probes used in glm fit.

missingValueSuppression

difference in ddG between the lowest fit beta values and estimates of betas for features that do not occur in the design matrix passed to glm fit.

minSeedValue

minimum value for mono-nucleotide affinities specified in initial seeding PSAM. If no value is specified explicitly, minSeedValue = 0.

regressionFormula

regression formula ('character' class) specifying the feature design of the 'model' object.

iteration

number of glm iterations performed.

upFootprintExtend

number of upstream base pairs to consider beyond the seed.

downFootprintExtend

number of downstream base pairs to consider beyond the seed.

rcSymmetric

boolean indicating whether of not a reverse complement symmetric model should be fit.

includeDNAstrand

boolean indicating whether or not a strand orientation specific offset should be included in the 'model' fit. If includeView == TRUE, includeDNAstrand is ignored.

includeView

boolean indicating whether or not a view+strand orientation specific offset should be included in the 'model' fit. If includeView == TRUE and rcSymmetric == TRUE, view offsets will be fit for only one of the two DNA strand orientations.

includeShape

boolean indicating whether or not shape coefficients should be included in the 'model' fit.

useFixedValuesOffset.N

logical: use initial, fixed values for mononucleotide positions within the model footprint, but not in N.set, as an offset to glm fit.

useFixedValuesOffset.Shape

logical: use initial, fixed values for shape positions within the model footprint, but not in Shape.set, as an offset to glm fit.

exUpBases

number of bases upstream of the mono-nucleotide position required to describe shape at the same position. If no value is specified explicitly, exUpBases = 2.

exDownBases

number of bases downstream of the mono-nucleotide position required to describe shape at the same position. If no value is specified explicitly, exDownBases = 2.

fpLen

footprint length of model. Must be fpLen = upFootprintExtend+seedLen+downFootprintExtend.

shapeParamsUsed

list of length one contaning a vector of shape features to be included in 'model'. Only used if includeShape == TRUE.

shapeTable

table of shape parameters to be used as predictors. Only used if includeShape == TRUE.

features

object of class 'featureSet' containing specifics of model design and values for model parameters.

verbose

logical: indicates whether to use verbose options in SelexGLM functions.

dateInitialized

Character string generated by date() at the time when the object of class 'model' is created.

dateBetasLastAdded

Character string generated by date() at the time when the object of class 'model' was last changed to incorporate new beta values.

dateLastModified

Character string generated by date() at the time when the object of class 'model' was changed using any of the methods associated with it.


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