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_zoom1 | aba.int_zoom1 - Internal fxn for 'aba.zoom' |
| aba.int_zoom2 | aba.int_zoom2 - Internal fxn for 'aba.zoom' |
| aba.plot | aba.plot() - Plot aba results |
| aba.query | aba.query() - Query aba results for all positive results |
| aba.save | aba.save - save 'aba.wrapper' figures |
| aba.wrapper | aba.wrapper - single function to query and plot the aba... |
| aba.zoom | aba.zoom - A function to help zoom in on specific data from... |
| 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... |
| add_ssh_known_host | add_ssh_known_host |
| adiponectin.scores | Genetic risk score for adiponectin and effects on coronary... |
| 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... |
| annot | Query analysis, variant, gene etc. annotation |
| aoex1 | Example dataset 1 |
| big_copy_to | Copy large data to RDIP tables. |
| binarise | Derive zero-or-one binary variable |
| blockassoc | Association tests for blocks of genotypes (one by one) |
| bp.scores | Genetic risk scores for blood pressure. |
| cad.scores | Genetic risk scores for coronary artery disease risk |
| chi2ncp | Compute non-centrality parameter of chi squared distribution. |
| CLEO | Conditional Leave-Each-Out (CLEO) analyses |
| clinex | Simulated example clinical trial data. |
| clinical.derive | Derive analysis variables from clinical data |
| clinical.import | Import multiple files exported from SAS |
| close_int_conn | Close connections they were internally created |
| coeff.extract | Coefficient extractor for fitted models. |
| coloc | Colocalization analysis. |
| coloc.compute | Colocalization computation |
| coloc.fast | Calculate colocalisation probabilities. |
| coloc_old | Colocalization analysis |
| combine.moments2 | Builds a matrix of second moments for a set of individuals,... |
| config_db | config_db |
| config_tmp_write_db | config_tmp_write_db |
| contrasting.rainbow | Rainbow of colours permuted to maximise contrast. |
| credset | Determine whether a SNP is in the credible set |
| demographics | Easy demographics tables. |
| derivation.add | Add a derivation |
| derivations.standard | Exploratory rules for deriving variables from clinical data |
| derivations.standard.IDSL | Rules for deriving variables from IDSL clinical data |
| drop_impala_copy | Drop (tmp) impala_copy_to tables. |
| est.moments2 | Estimate regression coefficients using quadratic... |
| find_qtl_bygene | Given an Ensembl ID, identify all significant QTLs |
| finitise | Ensure numeric values are finite |
| 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... |
| fixNA | Fix NA Table Row and Column Names |
| fupower | Power for followup studies |
| gclambda | Compute genomic control coefficient |
| gencode14.UGT1A1 | GENCODE14 data for region around the UGT1A1 gene. |
| gene | Annotate genomic positions with gene transcript information |
| gls.approx.logistic | Calculate weights and transformed phenotype so that one... |
| grade | Convert numeric values to ordinal grades |
| 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. |
| gtxanalyses | Find GWAS analyses |
| gtxcache | Speed up search of genes and analyses |
| gtx_debug | gtx_debug |
| gtx_error | gtx_error |
| gtx_fatal | gtx_fatal |
| gtx_fatal_stop | gtx_fatal_stop |
| gtx_info | gtx_info |
| gtx-package | Genetics ToolboX |
| gtx.params | Parameter format for multi-SNP analyses |
| gtxpipe | Pipeline for routine genetic association analysis and... |
| gtxregion | Interface to define a genomic region |
| gtxversion | gtxversion - Report GTX package info |
| gtx.version | Detailed package version information |
| gtx_warn | gtx_warn |
| gwas | GWAS summary |
| gwas2 | GWAS pairwise comparison |
| hapmap.read.haplotypes | Read hapmap haplotypes. |
| hapmap.snpdata | Extract individual level snp/haplotype data from HapMap |
| height.scores | Genetic risk score for height. |
| ideas_get_states | ideas_get_states |
| ideas_gwas_plot | ideas_gwas_plot |
| ideas_gwas_summarize | ideas_gwas_summarize |
| ideas_lasso | ideas_lasso |
| ideas_loci_summarize | ideas_loci_summarize |
| ideas_make | Ideas make |
| ideas_predict | ideas_predict |
| ideas_preload_states | ideas_preload_states |
| ideas_sum_pp_cross_cell_types | ideas_sum_pp_cross_cell_types |
| ideas_wrapper | ideas_preload_states |
| ile | Split data at tertiles, quartiles etc |
| impala_copy_to | Copy data to user's home database for joins with impala... |
| int_coloc_pics_lite | int_coloc_pics_lite Test for colocalization of two PICS sets |
| int_fastDoCall | An Alternative To The Internal Do.Call The do.call can be... |
| int_harmonize_pics | int_harmonize_pics |
| int_sbind | Combine Shape Objects |
| kmplot | Plot survival functions by discrete categories |
| landmark | Cuts survival object using (subject-specific) landmark times |
| 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. |
| manhattan | Manhattan plots for P-values |
| mincover | Compute minimum size of cover of overlapping intervals. |
| mlog10p | Negative log10 P values |
| moments2 | Class for summary statistic matrix of second moments. |
| mps.driver | Driver function for Modular Power Simulations |
| mps.simple | Simple Simulation Modules (ssm) for Illustrating Modular... |
| mthfrex | Simulated example finemapping genotype and phenotype data. |
| multicoloc | Multiple colocalization analyses |
| multicoloc2 | Multiple colocalization, use case 2 |
| multimatch | Match with multiple matching possible. |
| multipheno.OBrien | Multi-phenotype 1 df test for association |
| multipheno.T2 | Multi-phenotype test for association |
| n.extract | Sample size extractor for fitted models. |
| norm1 | Normalise to sum to 1. |
| otplot | Plot a factor variable by discrete categories |
| parse.snps | Parse text representation of a SNP embedded in flanking... |
| pcaplot | Principal component plot coloured by factor |
| pgx.endpoints | Derive pharmacogenetic (PGx) safety endpoints from... |
| pgx.exposure | Derive variables about treatment exposure from longitudinal... |
| pgx.trtreat | Derive time in relation to treatment. |
| phewas | Phenome Wide Assocation Study |
| piccolo | PICCOLO: Colocalization of GWAS and eQTL/pQTL signals without... |
| pics_calc | PICS calculation using the linkage information of 10,000 UKB... |
| plantation | Plantation (regular forest) plot |
| plotpos.by.chr | Utilities for Manhatten plots |
| positivise | Ensure numeric values are positive |
| prettye | Convert scientific notation to pretty expressions |
| prettypc | Pretty print percentages |
| prune.distance | Prune markers by physical position |
| prune.genes | Prune markers by physical position |
| qq10 | QQ plots on -log10 scale for p-values |
| qtplot | Plot a continuous variable by discrete categories |
| 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. |
| regionplot | Regional association plot |
| remap.q2t | Remap coordinates from BLAT query sequence to BLAT target... |
| replaceNA | Replace NA with something else |
| retrieve_data | Retrieve data for forest plots |
| safe | Safely apply a function |
| sanitise.whitespace | Remove leading and trailing spaces and convert multiple 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... |
| Surv2 | Construct survival object from event and would-be-censored... |
| t2dex | Simulated example genotype and longitudinal phenotype data. |
| t2d.scores | Genetic risk scores for type 2 diabetes risk. |
| test.extract | Test statistic extractor. |
| test.subsample | Test approximation used in genetic risk score analyses. |
| text2factor | Convert text to factor |
| textgrid | Add matrix of scaled text to a plot |
| tokenise.whitespace | Extract whitespace separated tokens |
| trial.params | Calculate Parameters for a Simple Model of a Clinical Trial |
| twopq | Calculate binomial variance 2p(1-p) |
| validate_impala | Validate and/or establish an impala odbc connection |
| validate_module_input | Validate module input has been changed |
| validate_sc | Validate and/or establish a spark connection |
| valuesof | Convert character vector to scalar |
| waterfall | Waterfall plot coloured by discrete categories |
| whoami | whoami - Determine user name/id for working with CDH. |
| zise | Normal quantile transform data |
