model-class: Class model for SelexGLM
In BussemakerLab/SelexGLM: Functions for performing feature-based analyis of SELEX-seq data using generalized linear models
Description
An S4 class to represent model object to store library design, model design, and model parameters for a SelexGLM project.
Slots
nameName to be associated with the model object. If unspecified, empty string is assigned by default.
varRegLenLength of the library design for the selex data.
leftFixedSeqFixed sequence to the left of random library in library design.
rightFixedSeqFixed sequence to the right of random library in library design.
seedLenLength of k-mer used to seed the regression. If unspecified, empty numeric value is assigned by default.
consensusSeqOptional 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.
leftFixedSeqOverlapNumber of bp into the left fixed flank to be considered in analysis. If unspecified, 0 is assigned by default.
rightFixedSeqOverlapNumber of bp into the right fixed flank to be considered in analysis. If unspecified, rightFixedSeqOverlap is set to leftFixedSeqOverlap by default.
affinityTypename of affinity variable in k-mer table to be used in building the seeding PSAM. If no value is specified, affinityType = 'Affinity'.
numViewsnumber of distinct views of length k contained in each strand. Must be equal to leftFixedSeqOverlap+varRegLen+rightFixedSeqOverlap.
roundslist of length 1 with rounds[[1]] equal to a vector containing the rounds of data to be fit.
confidenceLevelview confidence level cutoff required for probes used in glm fit.
minAffinityminimum view affinity required for probes used in glm fit.
missingValueSuppressiondifference 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.
minSeedValueminimum value for mono-nucleotide affinities specified in initial seeding PSAM. If no value is specified explicitly, minSeedValue = 0.
regressionFormularegression formula ('character' class) specifying the feature design of the 'model' object.
iterationnumber of glm iterations performed.
upFootprintExtendnumber of upstream base pairs to consider beyond the seed.
downFootprintExtendnumber of downstream base pairs to consider beyond the seed.
rcSymmetricboolean indicating whether of not a reverse complement symmetric model should be fit.
includeDNAstrandboolean indicating whether or not a strand orientation specific offset should be included in the 'model' fit. If includeView == TRUE, includeDNAstrand is ignored.
includeViewboolean 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.
includeShapeboolean indicating whether or not shape coefficients should be included in the 'model' fit.
useFixedValuesOffset.Nlogical: use initial, fixed values for mononucleotide positions within the model footprint, but not in N.set, as an offset to glm fit.
useFixedValuesOffset.Shapelogical: use initial, fixed values for shape positions within the model footprint, but not in Shape.set, as an offset to glm fit.
exUpBasesnumber of bases upstream of the mono-nucleotide position required to describe shape at the same position. If no value is specified explicitly, exUpBases = 2.
exDownBasesnumber of bases downstream of the mono-nucleotide position required to describe shape at the same position. If no value is specified explicitly, exDownBases = 2.
fpLenfootprint length of model. Must be fpLen = upFootprintExtend+seedLen+downFootprintExtend.
shapeParamsUsedlist of length one contaning a vector of shape features to be included in 'model'. Only used if includeShape == TRUE.
shapeTabletable of shape parameters to be used as predictors. Only used if includeShape == TRUE.
featuresobject of class 'featureSet' containing specifics of model design and values for model parameters.
verboselogical: indicates whether to use verbose options in SelexGLM functions.
dateInitializedCharacter string generated by date() at the time when the object of class 'model' is created.
dateBetasLastAddedCharacter string generated by date() at the time when the object of class 'model' was last changed to incorporate new beta values.
dateLastModifiedCharacter 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.
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Description
An S4 class to represent model object to store library design, model design, and model parameters for a SelexGLM project.
Slots
nameName to be associated with the model object. If unspecified, empty string is assigned by default.
varRegLenLength of the library design for the selex data.
leftFixedSeqFixed sequence to the left of random library in library design.
rightFixedSeqFixed sequence to the right of random library in library design.
seedLenLength of k-mer used to seed the regression. If unspecified, empty numeric value is assigned by default.
consensusSeqOptional 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.
leftFixedSeqOverlapNumber of bp into the left fixed flank to be considered in analysis. If unspecified, 0 is assigned by default.
rightFixedSeqOverlapNumber of bp into the right fixed flank to be considered in analysis. If unspecified,
rightFixedSeqOverlapis set toleftFixedSeqOverlapby default.affinityTypename of affinity variable in k-mer table to be used in building the seeding PSAM. If no value is specified, affinityType = 'Affinity'.
numViewsnumber of distinct views of length k contained in each strand. Must be equal to leftFixedSeqOverlap+varRegLen+rightFixedSeqOverlap.
roundslist of length 1 with rounds[[1]] equal to a vector containing the rounds of data to be fit.
confidenceLevelview confidence level cutoff required for probes used in glm fit.
minAffinityminimum view affinity required for probes used in glm fit.
missingValueSuppressiondifference 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.
minSeedValueminimum value for mono-nucleotide affinities specified in initial seeding PSAM. If no value is specified explicitly, minSeedValue = 0.
regressionFormularegression formula ('character' class) specifying the feature design of the 'model' object.
iterationnumber of glm iterations performed.
upFootprintExtendnumber of upstream base pairs to consider beyond the seed.
downFootprintExtendnumber of downstream base pairs to consider beyond the seed.
rcSymmetricboolean indicating whether of not a reverse complement symmetric model should be fit.
includeDNAstrandboolean indicating whether or not a strand orientation specific offset should be included in the 'model' fit. If includeView == TRUE, includeDNAstrand is ignored.
includeViewboolean 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.
includeShapeboolean indicating whether or not shape coefficients should be included in the 'model' fit.
useFixedValuesOffset.Nlogical: use initial, fixed values for mononucleotide positions within the model footprint, but not in N.set, as an offset to glm fit.
useFixedValuesOffset.Shapelogical: use initial, fixed values for shape positions within the model footprint, but not in Shape.set, as an offset to glm fit.
exUpBasesnumber of bases upstream of the mono-nucleotide position required to describe shape at the same position. If no value is specified explicitly, exUpBases = 2.
exDownBasesnumber of bases downstream of the mono-nucleotide position required to describe shape at the same position. If no value is specified explicitly, exDownBases = 2.
fpLenfootprint length of model. Must be fpLen = upFootprintExtend+seedLen+downFootprintExtend.
shapeParamsUsedlist of length one contaning a vector of shape features to be included in 'model'. Only used if includeShape == TRUE.
shapeTabletable of shape parameters to be used as predictors. Only used if includeShape == TRUE.
featuresobject of class 'featureSet' containing specifics of model design and values for model parameters.
verboselogical: indicates whether to use verbose options in SelexGLM functions.
dateInitializedCharacter string generated by date() at the time when the object of class 'model' is created.
dateBetasLastAddedCharacter string generated by date() at the time when the object of class 'model' was last changed to incorporate new beta values.
dateLastModifiedCharacter string generated by date() at the time when the object of class 'model' was changed using any of the methods associated with it.
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