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HapEstXXR (version 0.1-8)

Multi-Locus Stepwise Regression

Description

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).

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Version

Install

install.packages('HapEstXXR')

Monthly Downloads

30

Version

0.1-8

License

LGPL (>= 2.1)

Maintainer

Sven Knueppel

Last Published

June 2nd, 2015

Functions in HapEstXXR (0.1-8)

makeHaploviewInputFile

Make Haploview input files
HapEstXXR-package

Mulit-locus stepwise regression (MSR)
multi.snp.test

Internal function used for multi-locus associations tests.
allele1to2

Convert genotype matrix from two different types
dec2bin

Decimal To Binary Conversion
itegeppXXR

Haplotype estimation routine for single individual data
msr

Multi-locus stepwise regression
read.haploview

Read a haploview dataset
makePlinkInputFile

Make PLINK input files
coding.baseline.allele

Standardization of coding alleles
catt

Cochrane armitage trend test (CATT) for SNP genotypes
read.data

Read data from different input files
order.families

Ordering of nuclear family data
single.snp.test

Regression analysis with single SNP genotypes as independent variable
powerset

Generating power set of a set
maf

Minor alle frequencies
single.haplotype.test

single haplotype test