LocalSelect: Model for identifying erroneously linked pairs

In npcooley/Heron: A Package of Various Genomics Tools

Description

Though the function PairSummaries provides an argument allowing users to ask for alignments, given the time consuming nature of that process on large datasets, models are provided which allow for the quick and efficient identification of pairs whose PID would likely fall within a random distribution of PIDs.

Usage

data("LocalSelect")

Format

The format is: List of 21 $ coefficients : Named num [1:32] 1.2898 65.8948 -22.4148 -0.0031 -6.7246 ... ..- attr(*, "names")= chr [1:32] "(Intercept)" "MaxCoverage" "MinCoverage" "ExactMatch" ... $ R : num [1:32, 1:32] -61 0 0 0 0 ... ..- attr(*, "dimnames")=List of 2 .. ..$ : chr [1:32] "(Intercept)" "MaxCoverage" "MinCoverage" "ExactMatch" ... .. ..$ : chr [1:32] "(Intercept)" "MaxCoverage" "MinCoverage" "ExactMatch" ... $ rank : int 32 $ qr :List of 4 ..$ rank : int 32 ..$ qraux: num [1:32] 1 1 1 1 1 ... ..$ pivot: int [1:32] 1 2 3 4 5 6 7 8 9 10 ... ..$ tol : num 1e-11 ..- attr(*, "class")= chr "qr" $ family :List of 7 ..$ family : chr "binomial" ..$ link : chr "logit" ..$ linkfun :function (mu) ..$ linkinv :function (eta) ..$ mu.eta :function (eta) ..$ initialize: expression( if (NCOL(y) == 1) if (is.factor(y)) y <- y != levels(y)[1L] n <- rep.int(1, nobs) y[weights =| __truncated__ ..$ valideta :function (eta) ..- attr(*, "class")= chr "family" $ deviance : num 29193 $ aic : num 29257 $ null.deviance: num 73067 $ iter : int 9 $ df.residual : int 196744 $ df.null : int 196775 $ converged : logi TRUE $ boundary : logi FALSE $ call : language glm(formula = as.formula(LocalModels[[1]][[31]]), family = binomial(link = "logit"), data = TrainingTable02) $ formula :Class 'formula' language LocalCode ~ MaxCoverage * MinCoverage * ExactMatch * NormDeltaStart * NormDeltaStop $ terms :Classes 'terms', 'formula' language LocalCode ~ MaxCoverage * MinCoverage * ExactMatch * NormDeltaStart * NormDeltaStop .. ..- attr(*, "variables")= language list(LocalCode, MaxCoverage, MinCoverage, ExactMatch, NormDeltaStart, NormDeltaStop) .. ..- attr(*, "factors")= int [1:6, 1:31] 0 1 0 0 0 0 0 0 1 0 ... .. .. ..- attr(*, "dimnames")=List of 2 .. .. .. ..$ : chr [1:6] "LocalCode" "MaxCoverage" "MinCoverage" "ExactMatch" ... .. .. .. ..$ : chr [1:31] "MaxCoverage" "MinCoverage" "ExactMatch" "NormDeltaStart" ... .. ..- attr(*, "term.labels")= chr [1:31] "MaxCoverage" "MinCoverage" "ExactMatch" "NormDeltaStart" ... .. ..- attr(*, "order")= int [1:31] 1 1 1 1 1 2 2 2 2 2 ... .. ..- attr(*, "intercept")= int 1 .. ..- attr(*, "response")= int 1 .. ..- attr(*, "predvars")= language list(LocalCode, MaxCoverage, MinCoverage, ExactMatch, NormDeltaStart, NormDeltaStop) .. ..- attr(*, "dataClasses")= Named chr [1:6] "numeric" "numeric" "numeric" "numeric" ... .. .. ..- attr(*, "names")= chr [1:6] "LocalCode" "MaxCoverage" "MinCoverage" "ExactMatch" ... $ offset : NULL $ control :List of 3 ..$ epsilon: num 1e-08 ..$ maxit : num 25 ..$ trace : logi FALSE $ method : chr "glm.fit" $ contrasts : NULL $ xlevels : Named list() - attr(*, "class")= chr [1:2] "glm" "lm"

Details

A model for rejecting identified pairs whose link statistics indicate a likely local PID that would fall within a random distribution in an amino acid alignment.

Examples

data(LocalSelect)

npcooley/Heron documentation built on April 4, 2020, 10:24 p.m.