scrime v1.3.5

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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.

Functions in scrime

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

Type Package
Date 2018-12-01
License GPL-2
NeedsCompilation no
Packaged 2018-12-01 10:36:18 UTC; schwender
Repository CRAN
Date/Publication 2018-12-01 11:00:03 UTC

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