HapEstXXR: Multi-Locus Stepwise Regression
Version 0.1-8

The multi-locus stepwise regression (MSR) combines the advantages of stepwise regression and haplotype-based analysis. The MSR can be used to identify informative combinations of single nucleotide polymorphisms (SNPs) from unlinked SNPs (allele combinations) or SNPs within a chromosomal region (haplotypes).

AuthorSven Knueppel and Klaus Rohde
Date of publication2015-06-02 16:36:52
MaintainerSven Knueppel <sven.knueppel@dife.de>
LicenseLGPL (>= 2.1)
Version0.1-8
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("HapEstXXR")

Getting started

Package overview

Popular man pages

catt: Cochrane armitage trend test (CATT) for SNP genotypes
itegeppXXR: Haplotype estimation routine for single individual data
maf: Minor alle frequencies
makeHaploviewInputFile: Make Haploview input files
makePlinkInputFile: Make PLINK input files
read.haploview: Read a haploview dataset
single.haplotype.test: single haplotype test
See all...

All man pages Function index File listing

Man pages

allele1to2: Convert genotype matrix from two different types
catt: Cochrane armitage trend test (CATT) for SNP genotypes
coding.baseline.allele: Standardization of coding alleles
dec2bin: Decimal To Binary Conversion
HapEstXXR-package: Mulit-locus stepwise regression (MSR)
itegeppXXR: Haplotype estimation routine for single individual data
maf: Minor alle frequencies
makeHaploviewInputFile: Make Haploview input files
makePlinkInputFile: Make PLINK input files
msr: Multi-locus stepwise regression
multi.snp.test: Internal function used for multi-locus associations tests.
order.families: Ordering of nuclear family data
powerset: Generating power set of a set
read.data: Read data from different input files
read.haploview: Read a haploview dataset
single.haplotype.test: single haplotype test
single.snp.test: Regression analysis with single SNP genotypes as independent...

Functions

HapEstXXR Man page
HapEstXXR-package Man page
allele1to2 Man page Source code
allele1toR Man page Source code
allele2to1 Man page Source code
allele2toR Man page Source code
alleleRto1 Man page Source code
alleleRto2 Man page Source code
catt Man page Source code
coding.baseline.allele Man page Source code
dec2bin Man page Source code
hapest.caco Man page Source code
hapest.gaussian Man page Source code
itegeppXXR Man page Source code
maf Man page Source code
makeHaploviewInputFile Man page Source code
makePlinkInputFile Man page Source code
msr Man page Source code
msr.binomial.forward.adjusted Man page Source code
msr.binomial.forward.unadjusted Man page Source code
msr.binomial.haplotype.test.adjusted Man page Source code
msr.binomial.haplotype.test.unadjusted Man page Source code
msr.families.unadjusted Man page Source code
msr.gaussian.forward.adjusted Man page Source code
msr.gaussian.forward.unadjusted Man page Source code
msr.gaussian.haplotype.test.adjusted Man page Source code
msr.gaussian.haplotype.test.unadjusted Man page Source code
multi.snp.test Man page Source code
onLoad Source code
onUnLoad Source code
order.families Man page Source code
powerset Man page Source code
read.data Man page Source code
read.haploview Man page Source code
single.haplotype.test Man page Source code
single.haplotype.test.binomial Man page Source code
single.haplotype.test.families Man page Source code
single.haplotype.test.gaussian Man page Source code
single.haplotype.test.survival Man page
single.snp.test Man page Source code
single.snp.test.binomial Man page Source code
single.snp.test.casecohort Man page Source code
single.snp.test.casecohort.prentice Man page Source code
single.snp.test.families Man page Source code
single.snp.test.gaussian Man page Source code

Files

src
src/matrix.c
src/exist_pattern.c
src/messageR.h
src/powerset.c
src/itegeppXXR.c
src/readin.h
src/message.c
src/nrutil.h
src/rng.c
src/message.h
src/matalloc.c
src/longhap.h
src/quicksort.c
src/bool.h
src/readin.c
src/quicksort.h
src/create_pattern_matrix.c
src/matalloc.h
src/i_quicksort.c
src/fundamental.h
src/rng.h
src/haptdpnZR.c
src/matrix.h
src/HapRshort.c
NAMESPACE
R
R/msr.R
R/single.snp.test.casecohort.prentice.R
R/allele2toR.R
R/alleleRto2.R
R/single.snp.test.binomial.R
R/allele2to1.R
R/hapest.caco.R
R/catt.R
R/itegeppXXR.R
R/msr.gaussian.haplotype.test.adjusted.R
R/msr.binomial.haplotype.test.unadjusted.R
R/allele1toR.R
R/single.snp.test.families.R
R/makePlinkInputFile.R
R/powerset.R
R/msr.families.unadjusted.R
R/msr.binomial.forward.adjusted.R
R/multi.snp.test.R
R/msr.gaussian.forward.unadjusted.R
R/read.haploview.R
R/msr.binomial.haplotype.test.adjusted.R
R/coding.baseline.allele.R
R/order.families.R
R/single.haplotype.test.R
R/hapest.gaussian.R
R/msr.binomial.forward.unadjusted.R
R/msr.gaussian.forward.adjusted.R
R/msr.gaussian.haplotype.test.unadjusted.R
R/makeHaploviewInputFile.R
R/single.haplotype.test.gaussian.R
R/zzz.r
R/alleleRto1.R
R/single.snp.test.casecohort.R
R/single.haplotype.test.binomial.R
R/dec2bin.R
R/allele1to2.R
R/single.snp.test.R
R/maf.R
R/read.data.R
R/single.snp.test.gaussian.R
R/single.haplotype.test.families.R
MD5
DESCRIPTION
man
man/powerset.Rd
man/single.snp.test.Rd
man/HapEstXXR-package.Rd
man/multi.snp.test.Rd
man/makeHaploviewInputFile.Rd
man/single.haplotype.test.Rd
man/msr.Rd
man/makePlinkInputFile.Rd
man/coding.baseline.allele.Rd
man/allele1to2.Rd
man/order.families.Rd
man/read.data.Rd
man/maf.Rd
man/read.haploview.Rd
man/dec2bin.Rd
man/catt.Rd
man/itegeppXXR.Rd
HapEstXXR documentation built on May 19, 2017, 11:46 a.m.

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