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

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.

AuthorHolger Schwender, with a contribution of Arno Fritsch
Date of publication2013-09-02 00:22:22
MaintainerHolger Schwender <holger.schw@gmx.de>
LicenseGPL-2
Version1.3.3

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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