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.

Install the latest version of this package by entering the following in R:
install.packages("scrime")
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

Functions

abf Man page
analyse.models Man page
buildSNPannotation Man page
buildSNPmat Man page
canberra2Mats Man page
check4Monomorphism Man page
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
compChisqPval Man page
computeContCells Man page
computeContClass Man page
compVarLevs 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
gknn Man page
ia.samp Man page
identifyMonomorphism Man page
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
predictFBLR Man page
predict.pamCat Man page
print.colEpi Man page
print.pamCat Man page
print.simSNPcatResponse Man page
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
rowFreqs Man page
rowHWEs Man page
rowMAFs Man page
rowMsquares Man page
rowScales Man page
rowTables Man page
rowTrendFuzzy Man page
rowTrendStats Man page
sample.snpmat Man page
shortenGeneDescription Man page
showChanges Man page
simulateSNPcatResponse Man page
simulateSNPglm Man page
simulateSNPs Man page
smc Man page
smc2Mats Man page
snp1norm2Mats Man page
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

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

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.