gtx: Genetics ToolboX

Assorted tools for genetic association analyses. The current focus is on implementing (either exactly or approximately) regression analyses using summary statistics instead of using subject-specific data. So far, functions exist to support multi-SNP risk score analyses, multi-SNP conditional regression analyses, and multi-phenotype analyses, using summary statistics. There are helper functions for reading and manipulating subject-specific genotype data, which provide a platform for calculating the summary statistics, or for using R to conduct other analyses not supported by specific GWAS analysis tools.

AuthorToby Johnson <Toby.x.Johnson@gsk.com>
Date of publication2013-01-11 12:26:06
MaintainerToby Johnson <Toby.x.Johnson@gsk.com>
LicenseGPL (>= 2)
Version0.0.8

View on CRAN

Man pages

abf.normal: Calculate approximate Bayes factor (ABF) for normal prior.

abf.t: Calculate approximate Bayes factor (ABF) for t distribution...

abf.Wakefield: Calculate approximate Bayes factor (ABF) using method of...

agtstats: Hypertension association statistics for SNPs near the AGT...

align.snpdata.coding: Update genotype coding when there are coded allele...

allelesAB: Paste together (vectors of) A and B alleles after sorting...

bp.scores: Genetic risk scores for blood pressure.

cad.scores: Genetic risk scores for coronary artery disease risk

coeff.extract: Coefficient extractor for fitted models.

combine.moments2: Builds a matrix of second moments for a set of individuals,...

contrasting.rainbow: Rainbow of colours permuted to maximise contrast.

est.moments2: Estimate regression coefficients using quadratic...

fitmix: Fit finite mixture of univariate Gaussian densities to data.

fitmix.plot: Plot empirical density and components and total density for...

fitmix.r2: For finite mixture of univariate Gaussian densities, computes...

fitmix.simulate: Simulate from finite mixture of univariate Gaussian...

gls.approx.logistic: Calculate weights and transformed phenotype so that one...

grs.filter.Qrs: Filter SNPs for inclusion in genetic risk score using...

grs.make.scores: Make genetic risk scores from individual-level data.

grs.onesnp.apply: Convenience tool to fit a series of single-SNP models.

grs.plot: Diagnostic plot for genetic risk score calculation from...

grs.summary: Genetic risk score calculation from summary statistics.

gtx-package: Genetics ToolboX

gtx.params: Parameter format for multi-SNP analyses

hapmap.read.haplotypes: Read hapmap haplotypes.

hapmap.snpdata: Extract individual level snp/haplotype data from HapMap

height.scores: Genetic risk score for height.

lipid.cad.scores: Genetic risk scores for serum lipid levels and coronary...

lipid.scores: Genetic risk scores for serum lipid levels

liver.scores: Genetic risk scores for liver enzyme traits.

lm.moments2: Fit normal linear model using pre-built matrix of second...

magic.scores: Genetic risk scores for glucose/insulin traits.

make.moments2: Build matrix of second moments from subject-specific data.

mincover: Compute minimum size of cover of overlapping intervals.

moments2: Class for summary statistic matrix of second moments.

mthfrex: Simulated example finemapping genotype and phenotype data.

multimatch: Match with multiple matching possible.

multipheno.T2: Multi-phenotype test for association

ncp: Compute non-centrality parameter of chi squared distribution.

parse.snps: Parse text representation of a SNP embedded in flanking...

read.snpdata.impute: Read genotype dosages in the format output by IMPUTE.

read.snpdata.mach: Read genotype dosages in the format output by MACH

read.snpdata.minimac: Read genotype dosages in the format output by minimac

read.snpdata.plink: Read genotype dosages in the format output by PLINK.

remap.q2t: Remap coordinates from BLAT query sequence to BLAT target...

sanitise.whitespace: Remove leading and trailing spaces; convert double spaces to...

snpdata: Class for SNP genotype and phenotype data.

snphwe: Exact test of Hardy-Weinberg.

snphweCounts: Exact test of Hardy-Weinberg.

snps.BRCA1: Genotyping array annotation for SNPs near the BRCA1 gene.

stepdown.moments2: Stepwise downward model selection using summary statistic...

stepup.moments2: Stepwise upward model selection using summary statistic...

t2dex: Simulated example genotype and longitudinal phenotype data.

t2d.scores: Genetic risk scores for type 2 diabetes risk.

test.subsample: Test approximation used in genetic risk score analyses.

Files in this package

gtx
gtx/MD5
gtx/vignettes
gtx/vignettes/ashg2012.Rnw
gtx/R
gtx/R/stepwise.R gtx/R/snphwe.R gtx/R/snpdata.R gtx/R/power.R gtx/R/multipheno.R gtx/R/multimatch.R gtx/R/moments2.R gtx/R/mincover.R gtx/R/manhatten.R gtx/R/input.R gtx/R/hapmap.R gtx/R/grs.R gtx/R/glsglm.R gtx/R/fitmix.R gtx/R/blat.R gtx/R/abf.R
gtx/NAMESPACE
gtx/man
gtx/man/test.subsample.Rd gtx/man/t2dex.Rd gtx/man/t2d.scores.Rd gtx/man/stepup.moments2.Rd gtx/man/stepdown.moments2.Rd gtx/man/snps.BRCA1.Rd gtx/man/snphweCounts.Rd gtx/man/snphwe.Rd gtx/man/snpdata.Rd gtx/man/sanitise.whitespace.Rd gtx/man/remap.q2t.Rd gtx/man/read.snpdata.plink.Rd gtx/man/read.snpdata.minimac.Rd gtx/man/read.snpdata.mach.Rd gtx/man/read.snpdata.impute.Rd gtx/man/parse.snps.Rd gtx/man/ncp.Rd gtx/man/multipheno.T2.Rd gtx/man/multimatch.Rd gtx/man/mthfrex.Rd gtx/man/moments2.Rd gtx/man/mincover.Rd gtx/man/make.moments2.Rd gtx/man/magic.scores.Rd gtx/man/lm.moments2.Rd gtx/man/liver.scores.Rd gtx/man/lipid.scores.Rd gtx/man/lipid.cad.scores.Rd gtx/man/height.scores.Rd gtx/man/hapmap.snpdata.Rd gtx/man/hapmap.read.haplotypes.Rd gtx/man/gtx.params.Rd gtx/man/gtx-package.Rd gtx/man/grs.summary.Rd gtx/man/grs.plot.Rd gtx/man/grs.onesnp.apply.Rd gtx/man/grs.make.scores.Rd gtx/man/grs.filter.Qrs.Rd gtx/man/gls.approx.logistic.Rd gtx/man/fitmix.simulate.Rd gtx/man/fitmix.Rd gtx/man/fitmix.r2.Rd gtx/man/fitmix.plot.Rd gtx/man/est.moments2.Rd gtx/man/contrasting.rainbow.Rd gtx/man/combine.moments2.Rd gtx/man/coeff.extract.Rd gtx/man/cad.scores.Rd gtx/man/bp.scores.Rd gtx/man/allelesAB.Rd gtx/man/align.snpdata.coding.Rd gtx/man/agtstats.Rd gtx/man/abf.Wakefield.Rd gtx/man/abf.t.Rd gtx/man/abf.normal.Rd
gtx/inst
gtx/inst/doc
gtx/inst/doc/ashg2012.Rnw
gtx/inst/doc/ashg2012.pdf
gtx/DESCRIPTION
gtx/data
gtx/data/t2dex.RData
gtx/data/t2d.scores.RData
gtx/data/snps.BRCA1.RData
gtx/data/mthfrex.RData
gtx/data/magic.scores.RData
gtx/data/liver.scores.RData
gtx/data/lipid.scores.RData
gtx/data/lipid.cad.scores.RData
gtx/data/height.scores.RData
gtx/data/cad.scores.RData
gtx/data/bp.scores.RData
gtx/data/agtstats.RData
gtx/ChangeLog

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

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