HapEstXXR: Multi-Locus Stepwise Regression

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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).

Author
Sven Knueppel and Klaus Rohde
Date of publication
2015-06-02 16:36:52
Maintainer
Sven Knueppel <sven.knueppel@dife.de>
License
LGPL (>= 2.1)
Version
0.1-8

View on CRAN

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...

Files in this package

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