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.

Author
Toby Johnson <Toby.x.Johnson@gsk.com>
Date of publication
2013-01-11 12:26:06
Maintainer
Toby Johnson <Toby.x.Johnson@gsk.com>
License
GPL (>= 2)
Version
0.0.8

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