scrime: Analysis of High-Dimensional Categorical Data such as SNP Data
Version 1.3.3

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.

Browse man pages Browse package API and functions Browse package files

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
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("scrime")

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

Functions

abf Man page Source code
allBetweenCombs Source code
allCombs Source code
analyse.models Man page
buildSNPannotation Man page Source code
buildSNPmat Man page Source code
canberra2Mats Man page
check4Monomorphism Man page Source code
checkATCG Man page
checkCatMat Man page
checkDist Man page
checkDistMat Man page
checkMatSNP Man page
checkX1X2 Man page
chisqClass2 Man page
chisqInd Man page
cohen Man page
cohen2Mats Man page
colEpistatic Man page Source code
compChisqPval Man page
compVarLevs Man page
computeContCells Man page
computeContClass Man page
constructMatCheck Man page
constructMatIA Man page
dist2Mats Man page
euclidean2Mats Man page
evalRedundancy Man page
fblr Man page
fblr.weight Man page
getBinDomRec Man page
getBinGenotype Man page
getCall Man page
getDistance Man page
getListIdentity Man page
getMatFuzzy Man page Source code
getResponseCat1 Source code
getResponseRef Source code
gknn Man page
ia.samp Man page
identifyMonomorphism Man page Source code
knncatimpute Man page
knncatimputeLarge Man page
manhattan2Mats Man page
maximum2Mats Man page
mc2Mats Man page
minkowski2Mats Man page
minrc Man page
minrc2Mats Man page
modeDist Man page
pamCat Man page
pcc Man page
pcc2Mats Man page
predict.pamCat Man page
predictFBLR Man page
print.colEpi Man page Source code
print.pamCat Man page
print.simSNPcatResponse Man page Source code
print.simSNPglm Man page
print.simulatedSNPs Man page
recodeAffySNP Man page
recodeCount Man page
recodeFirst Man page
recodeNoHete Man page
recodeSNPs Man page
removeRedundancy Man page
replaceNAs Man page
row2col Man page
rowCATTs Man page
rowChisq2Class Man page
rowChisqMultiClass Man page
rowChisqStats Man page
rowCors Man page
rowEpistatic Man page Source code
rowFreqs Man page
rowHWEs Man page Source code
rowMAFs Man page Source code
rowMsquares Man page
rowScales Man page
rowTables Man page
rowTrendFuzzy Man page Source code
rowTrendStats Man page
sample.snpmat Man page
shortenGeneDescription Man page Source code
showChanges Man page Source code
simulateSNPcatResponse Man page Source code
simulateSNPglm Man page
simulateSNPs Man page
smc Man page
smc2Mats Man page
snp1norm2Mats Man page Source code
snp2bin Man page
summary.simSNPglm Man page
weightMode Man page

Files

inst
inst/CHANGES
NAMESPACE
R
R/rowCATTs.R
R/check4Monomorphism.R
R/recodeSNPs.R
R/canberra2Mats.R
R/rowHWEs.R
R/getBinGenotype.R
R/row2col.R
R/checkDistMat.R
R/rowChisqMultiClass.R
R/mc2Mats.R
R/print.simSNPcatResponse.R
R/compVarLevs.R
R/checkTableList.R
R/getListIdentity.R
R/removeRedundancy.R
R/simulateSNPcatResponse.R
R/pcc.R
R/analyse.models.R
R/rowFreqs.R
R/evalRedundancy.R
R/simulateSNPglm.R
R/rowCors.R
R/computeContCells.R
R/print.simSNPglm.R
R/chisqInd.R
R/smc.R
R/cohen.R
R/abf.R
R/rowTrendFuzzy.R
R/compChisqPval.R
R/chisqClass2.R
R/print.pamCat.R
R/checkATCG.R
R/minrc2Mats.R
R/knncatimpute.R
R/pamCat.R
R/dist2Mats.R
R/recodeAffySNP.R
R/replaceNAs.R
R/fblr.weight.R
R/pcc2Mats.R
R/minkowski2Mats.R
R/rowScales.R
R/showChanges.R
R/modeDist.R
R/computeContClass.R
R/rowTrendStats.R
R/print.simulatedSNPs.R
R/checkX1X2.R
R/getCall.R
R/knncatimputeLarge.R
R/snp2bin.R
R/identifyMonomorphism.R
R/rowMsquares.R
R/snp1norm2Mats.R
R/weightMode.R
R/checkMatSNP.R
R/rowMAFs.R
R/recodeFirst.R
R/fblr.R
R/constructMatIA.R
R/summary.simSNPglm.R
R/recodeCount.R
R/getDistance.R
R/rowTables.R
R/getResponse.R
R/buildSNPannotation.R
R/checkCatMat.R
R/rowChisqStats.R
R/minrc.R
R/predictFBLR.R
R/ia.samp.R
R/getMatFuzzy.R
R/buildSNPmat.R
R/cohen2Mats.R
R/checkDist.R
R/gknn.R
R/rowChisq2Class.R
R/getBinDomRec.R
R/predict.pamCat.R
R/colEpistatic.R
R/constructMatCheck.R
R/sample.snpmat.R
R/manhattan2Mats.R
R/recodeNoHete.R
R/euclidean2Mats.R
R/smc2Mats.R
R/simulateSNPs.R
R/maximum2Mats.R
MD5
DESCRIPTION
man
man/computeContClass.Rd
man/fblr.Rd
man/rowMsquares.Rd
man/rowCATTs.Rd
man/rowTables.Rd
man/shortenGeneDescription.Rd
man/knncatimpute.Rd
man/rowScales.Rd
man/rowChisq2Class.Rd
man/rowMAFs.Rd
man/analyse.models.Rd
man/snp2bin.Rd
man/colEpistatic.Rd
man/rowCors.Rd
man/pamCat.Rd
man/computeContCells.Rd
man/simulateSNPs.Rd
man/rowTrendStats.Rd
man/rowChisqStats.Rd
man/buildSNPannotation.Rd
man/smc.Rd
man/rowTrendFuzzy.Rd
man/scrime-internal.Rd
man/pcc.Rd
man/predict.pamCat.Rd
man/abf.Rd
man/simulateSNPcatResponse.Rd
man/recodeAffySNP.Rd
man/showChanges.Rd
man/rowFreqs.Rd
man/recodeSNPs.Rd
man/summary.simSNPglm.Rd
man/rowHWEs.Rd
man/knncatimputeLarge.Rd
man/predictFBLR.Rd
man/simulateSNPglm.Rd
man/gknn.Rd
man/identifyMonomorphism.Rd
scrime documentation built on May 19, 2017, 4:36 p.m.