scrime: Analysis of High-Dimensional Categorical Data such as SNP Data

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Tools for the analysis of high-dimensional data developed/implemented at the group "Statistical Complexity Reduction In Molecular Epidemiology" (SCRIME). Main focus is on SNP data. But most of the functions can also be applied to other types of categorical data.

Author
Holger Schwender, with a contribution of Arno Fritsch
Date of publication
2013-09-02 00:22:22
Maintainer
Holger Schwender <holger.schw@gmx.de>
License
GPL-2
Version
1.3.3

View on CRAN

Man pages

abf
Approximate Bayes Factor
analyse.models
Summarize MCMC sample of Bayesian logic regression models
buildSNPannotation
Construct Annotation for Affymetrix SNP Chips
colEpistatic
Cordell's Test for Epistatic Interactions
computeContCells
Pairwise Contingency Tables
computeContClass
Rowwise Contigency Tables
fblr
Full Bayesian Logic Regression for SNP Data
gknn
Generalized k Nearest Neighbors
identifyMonomorphism
Identification of Constant Variables
knncatimpute
Missing Value Imputation with kNN
knncatimputeLarge
Missing Value Imputation with kNN for High-Dimensional Data
pamCat
Prediction Analysis of Categorical Data
pcc
Pearson's Contingency Coefficient
predictFBLR
Predict Case Probabilities with Full Bayesian Logic...
predict.pamCat
Predict Method for pamCat Objects
recodeAffySNP
Recoding of Affymetrix SNP Values
recodeSNPs
Recoding of SNP Values
rowCATTs
Rowwise Cochran-Armitage Trend Test Based on Tables
rowChisq2Class
Rowwise Pearson's ChiSquare Test Based on Tables
rowChisqStats
Rowwise Pearson's ChiSquare Statistic
rowCors
Rowwise Correlation with a Vector
rowFreqs
Rowwise Frequencies
rowHWEs
Rowwise Test for Hardy-Weinberg Equilibrium
rowMAFs
Rowwise Minor Allele Frequency
rowMsquares
Rowwise Linear Trend Test Based on Tables
rowScales
Rowwise Scaling
rowTables
Rowwise Tables
rowTrendFuzzy
Trend Test for Fuzzy Genotype Calls
rowTrendStats
Rowwise Linear Trend Tests
scrime-internal
Internal scrime functions
shortenGeneDescription
Shorten the Gene Description
showChanges
Displaying Changes
simulateSNPcatResponse
Simulation of SNP Data with Categorical Response
simulateSNPglm
Simulation of SNP data
simulateSNPs
Simulation of SNP data
smc
Simple Matching Coefficient and Cohen's Kappa
snp2bin
Transformation of SNPs to Binary Variables
summary.simSNPglm
Summarizing a simSNPglm object

Files in this package

scrime
scrime/inst
scrime/inst/CHANGES
scrime/NAMESPACE
scrime/R
scrime/R/rowCATTs.R
scrime/R/check4Monomorphism.R
scrime/R/recodeSNPs.R
scrime/R/canberra2Mats.R
scrime/R/rowHWEs.R
scrime/R/getBinGenotype.R
scrime/R/row2col.R
scrime/R/checkDistMat.R
scrime/R/rowChisqMultiClass.R
scrime/R/mc2Mats.R
scrime/R/print.simSNPcatResponse.R
scrime/R/compVarLevs.R
scrime/R/checkTableList.R
scrime/R/getListIdentity.R
scrime/R/removeRedundancy.R
scrime/R/simulateSNPcatResponse.R
scrime/R/pcc.R
scrime/R/analyse.models.R
scrime/R/rowFreqs.R
scrime/R/evalRedundancy.R
scrime/R/simulateSNPglm.R
scrime/R/rowCors.R
scrime/R/computeContCells.R
scrime/R/print.simSNPglm.R
scrime/R/chisqInd.R
scrime/R/smc.R
scrime/R/cohen.R
scrime/R/abf.R
scrime/R/rowTrendFuzzy.R
scrime/R/compChisqPval.R
scrime/R/chisqClass2.R
scrime/R/print.pamCat.R
scrime/R/checkATCG.R
scrime/R/minrc2Mats.R
scrime/R/knncatimpute.R
scrime/R/pamCat.R
scrime/R/dist2Mats.R
scrime/R/recodeAffySNP.R
scrime/R/replaceNAs.R
scrime/R/fblr.weight.R
scrime/R/pcc2Mats.R
scrime/R/minkowski2Mats.R
scrime/R/rowScales.R
scrime/R/showChanges.R
scrime/R/modeDist.R
scrime/R/computeContClass.R
scrime/R/rowTrendStats.R
scrime/R/print.simulatedSNPs.R
scrime/R/checkX1X2.R
scrime/R/getCall.R
scrime/R/knncatimputeLarge.R
scrime/R/snp2bin.R
scrime/R/identifyMonomorphism.R
scrime/R/rowMsquares.R
scrime/R/snp1norm2Mats.R
scrime/R/weightMode.R
scrime/R/checkMatSNP.R
scrime/R/rowMAFs.R
scrime/R/recodeFirst.R
scrime/R/fblr.R
scrime/R/constructMatIA.R
scrime/R/summary.simSNPglm.R
scrime/R/recodeCount.R
scrime/R/getDistance.R
scrime/R/rowTables.R
scrime/R/getResponse.R
scrime/R/buildSNPannotation.R
scrime/R/checkCatMat.R
scrime/R/rowChisqStats.R
scrime/R/minrc.R
scrime/R/predictFBLR.R
scrime/R/ia.samp.R
scrime/R/getMatFuzzy.R
scrime/R/buildSNPmat.R
scrime/R/cohen2Mats.R
scrime/R/checkDist.R
scrime/R/gknn.R
scrime/R/rowChisq2Class.R
scrime/R/getBinDomRec.R
scrime/R/predict.pamCat.R
scrime/R/colEpistatic.R
scrime/R/constructMatCheck.R
scrime/R/sample.snpmat.R
scrime/R/manhattan2Mats.R
scrime/R/recodeNoHete.R
scrime/R/euclidean2Mats.R
scrime/R/smc2Mats.R
scrime/R/simulateSNPs.R
scrime/R/maximum2Mats.R
scrime/MD5
scrime/DESCRIPTION
scrime/man
scrime/man/computeContClass.Rd
scrime/man/fblr.Rd
scrime/man/rowMsquares.Rd
scrime/man/rowCATTs.Rd
scrime/man/rowTables.Rd
scrime/man/shortenGeneDescription.Rd
scrime/man/knncatimpute.Rd
scrime/man/rowScales.Rd
scrime/man/rowChisq2Class.Rd
scrime/man/rowMAFs.Rd
scrime/man/analyse.models.Rd
scrime/man/snp2bin.Rd
scrime/man/colEpistatic.Rd
scrime/man/rowCors.Rd
scrime/man/pamCat.Rd
scrime/man/computeContCells.Rd
scrime/man/simulateSNPs.Rd
scrime/man/rowTrendStats.Rd
scrime/man/rowChisqStats.Rd
scrime/man/buildSNPannotation.Rd
scrime/man/smc.Rd
scrime/man/rowTrendFuzzy.Rd
scrime/man/scrime-internal.Rd
scrime/man/pcc.Rd
scrime/man/predict.pamCat.Rd
scrime/man/abf.Rd
scrime/man/simulateSNPcatResponse.Rd
scrime/man/recodeAffySNP.Rd
scrime/man/showChanges.Rd
scrime/man/rowFreqs.Rd
scrime/man/recodeSNPs.Rd
scrime/man/summary.simSNPglm.Rd
scrime/man/rowHWEs.Rd
scrime/man/knncatimputeLarge.Rd
scrime/man/predictFBLR.Rd
scrime/man/simulateSNPglm.Rd
scrime/man/gknn.Rd
scrime/man/identifyMonomorphism.Rd