Man pages for tobyjohnson/gtx
Genetics ToolboX

aba.fill*aba.fill() - Fill in missing data to complete matrix of...
aba.flatten*aba.flatten() - Flatten full aba results*
aba.int_coloc_plot*aba.int_coloc_plot() - Plot aba results*
aba.int_zoom1aba.int_zoom1 - Internal fxn for 'aba.zoom'
aba.int_zoom2aba.int_zoom2 - Internal fxn for 'aba.zoom'
aba.plotaba.plot() - Plot aba results
aba.queryaba.query() - Query aba results for all positive results
aba.saveaba.save - save 'aba.wrapper' figures
aba.wrapperaba.wrapper - single function to query and plot the aba...
aba.zoomaba.zoom - A function to help zoom in on specific data from...
abf.normalCalculate approximate Bayes factor (ABF) for normal prior.
abf.tCalculate approximate Bayes factor (ABF) for t distribution...
abf.WakefieldCalculate approximate Bayes factor (ABF) using method of...
add_ssh_known_hostadd_ssh_known_host
adiponectin.scoresGenetic risk score for adiponectin and effects on coronary...
agtstatsHypertension association statistics for SNPs near the AGT...
align.snpdata.codingUpdate genotype coding when there are coded allele...
allelesABPaste together (vectors of) A and B alleles after sorting...
annotQuery analysis, variant, gene etc. annotation
aoex1Example dataset 1
big_copy_toCopy large data to RDIP tables.
binariseDerive zero-or-one binary variable
blockassocAssociation tests for blocks of genotypes (one by one)
bp.scoresGenetic risk scores for blood pressure.
cad.scoresGenetic risk scores for coronary artery disease risk
chi2ncpCompute non-centrality parameter of chi squared distribution.
CLEOConditional Leave-Each-Out (CLEO) analyses
clinexSimulated example clinical trial data.
clinical.deriveDerive analysis variables from clinical data
clinical.importImport multiple files exported from SAS
close_int_connClose connections they were internally created
coeff.extractCoefficient extractor for fitted models.
colocColocalization analysis.
coloc.computeColocalization computation
coloc.fastCalculate colocalisation probabilities.
coloc_oldColocalization analysis
combine.moments2Builds a matrix of second moments for a set of individuals,...
config_dbconfig_db
config_tmp_write_dbconfig_tmp_write_db
contrasting.rainbowRainbow of colours permuted to maximise contrast.
credsetDetermine whether a SNP is in the credible set
demographicsEasy demographics tables.
derivation.addAdd a derivation
derivations.standardExploratory rules for deriving variables from clinical data
derivations.standard.IDSLRules for deriving variables from IDSL clinical data
drop_impala_copyDrop (tmp) impala_copy_to tables.
est.moments2Estimate regression coefficients using quadratic...
find_qtl_bygeneGiven an Ensembl ID, identify all significant QTLs
finitiseEnsure numeric values are finite
fitmixFit finite mixture of univariate Gaussian densities to data.
fitmix.plotPlot empirical density and components and total density for...
fitmix.r2For finite mixture of univariate Gaussian densities, computes...
fitmix.simulateSimulate from finite mixture of univariate Gaussian...
fixNAFix NA Table Row and Column Names
fupowerPower for followup studies
gclambdaCompute genomic control coefficient
gencode14.UGT1A1GENCODE14 data for region around the UGT1A1 gene.
geneAnnotate genomic positions with gene transcript information
gls.approx.logisticCalculate weights and transformed phenotype so that one...
gradeConvert numeric values to ordinal grades
grs.filter.QrsFilter SNPs for inclusion in genetic risk score using...
grs.make.scoresMake genetic risk scores from individual-level data.
grs.onesnp.applyConvenience tool to fit a series of single-SNP models.
grs.plotDiagnostic plot for genetic risk score calculation from...
grs.summaryGenetic risk score calculation from summary statistics.
gtxanalysesFind GWAS analyses
gtxcacheSpeed up search of genes and analyses
gtx_debuggtx_debug
gtx_errorgtx_error
gtx_fatalgtx_fatal
gtx_fatal_stopgtx_fatal_stop
gtx_infogtx_info
gtx-packageGenetics ToolboX
gtx.paramsParameter format for multi-SNP analyses
gtxpipePipeline for routine genetic association analysis and...
gtxregionInterface to define a genomic region
gtxversiongtxversion - Report GTX package info
gtx.versionDetailed package version information
gtx_warngtx_warn
gwasGWAS summary
gwas2GWAS pairwise comparison
hapmap.read.haplotypesRead hapmap haplotypes.
hapmap.snpdataExtract individual level snp/haplotype data from HapMap
height.scoresGenetic risk score for height.
ideas_get_statesideas_get_states
ideas_gwas_plotideas_gwas_plot
ideas_gwas_summarizeideas_gwas_summarize
ideas_lassoideas_lasso
ideas_loci_summarizeideas_loci_summarize
ideas_makeIdeas make
ideas_predictideas_predict
ideas_preload_statesideas_preload_states
ideas_sum_pp_cross_cell_typesideas_sum_pp_cross_cell_types
ideas_wrapperideas_preload_states
ileSplit data at tertiles, quartiles etc
impala_copy_toCopy data to user's home database for joins with impala...
int_coloc_pics_liteint_coloc_pics_lite Test for colocalization of two PICS sets
int_fastDoCallAn Alternative To The Internal Do.Call The do.call can be...
int_harmonize_picsint_harmonize_pics
int_sbindCombine Shape Objects
kmplotPlot survival functions by discrete categories
landmarkCuts survival object using (subject-specific) landmark times
lipid.cad.scoresGenetic risk scores for serum lipid levels and coronary...
lipid.scoresGenetic risk scores for serum lipid levels
liver.scoresGenetic risk scores for liver enzyme traits.
lm.moments2Fit normal linear model using pre-built matrix of second...
magic.scoresGenetic risk scores for glucose/insulin traits.
make.moments2Build matrix of second moments from subject-specific data.
manhattanManhattan plots for P-values
mincoverCompute minimum size of cover of overlapping intervals.
mlog10pNegative log10 P values
moments2Class for summary statistic matrix of second moments.
mps.driverDriver function for Modular Power Simulations
mps.simpleSimple Simulation Modules (ssm) for Illustrating Modular...
mthfrexSimulated example finemapping genotype and phenotype data.
multicolocMultiple colocalization analyses
multicoloc2Multiple colocalization, use case 2
multimatchMatch with multiple matching possible.
multipheno.OBrienMulti-phenotype 1 df test for association
multipheno.T2Multi-phenotype test for association
n.extractSample size extractor for fitted models.
norm1Normalise to sum to 1.
otplotPlot a factor variable by discrete categories
parse.snpsParse text representation of a SNP embedded in flanking...
pcaplotPrincipal component plot coloured by factor
pgx.endpointsDerive pharmacogenetic (PGx) safety endpoints from...
pgx.exposureDerive variables about treatment exposure from longitudinal...
pgx.trtreatDerive time in relation to treatment.
phewasPhenome Wide Assocation Study
piccoloPICCOLO: Colocalization of GWAS and eQTL/pQTL signals without...
pics_calcPICS calculation using the linkage information of 10,000 UKB...
plantationPlantation (regular forest) plot
plotpos.by.chrUtilities for Manhatten plots
positiviseEnsure numeric values are positive
prettyeConvert scientific notation to pretty expressions
prettypcPretty print percentages
prune.distancePrune markers by physical position
prune.genesPrune markers by physical position
qq10QQ plots on -log10 scale for p-values
qtplotPlot a continuous variable by discrete categories
read.snpdata.imputeRead genotype dosages in the format output by IMPUTE.
read.snpdata.machRead genotype dosages in the format output by MACH
read.snpdata.minimacRead genotype dosages in the format output by minimac
read.snpdata.plinkRead genotype dosages in the format output by PLINK.
regionplotRegional association plot
remap.q2tRemap coordinates from BLAT query sequence to BLAT target...
replaceNAReplace NA with something else
retrieve_dataRetrieve data for forest plots
safeSafely apply a function
sanitise.whitespaceRemove leading and trailing spaces and convert multiple to...
snpdataClass for SNP genotype and phenotype data.
snphweExact test of Hardy-Weinberg.
snphweCountsExact test of Hardy-Weinberg.
snps.BRCA1Genotyping array annotation for SNPs near the BRCA1 gene.
stepdown.moments2Stepwise downward model selection using summary statistic...
stepup.moments2Stepwise upward model selection using summary statistic...
Surv2Construct survival object from event and would-be-censored...
t2dexSimulated example genotype and longitudinal phenotype data.
t2d.scoresGenetic risk scores for type 2 diabetes risk.
test.extractTest statistic extractor.
test.subsampleTest approximation used in genetic risk score analyses.
text2factorConvert text to factor
textgridAdd matrix of scaled text to a plot
tokenise.whitespaceExtract whitespace separated tokens
trial.paramsCalculate Parameters for a Simple Model of a Clinical Trial
twopqCalculate binomial variance 2p(1-p)
validate_impalaValidate and/or establish an impala odbc connection
validate_module_inputValidate module input has been changed
validate_scValidate and/or establish a spark connection
valuesofConvert character vector to scalar
waterfallWaterfall plot coloured by discrete categories
whoamiwhoami - Determine user name/id for working with CDH.
ziseNormal quantile transform data
tobyjohnson/gtx documentation built on June 8, 2019, 1:32 p.m.