Package: hJAM 1.0.1

Lai Jiang

hJAM: Hierarchical Joint Analysis of Marginal Summary Statistics

Provides functions to implement a hierarchical approach which is designed to perform joint analysis of summary statistics using the framework of Mendelian Randomization or transcriptome analysis. Reference: Lai Jiang, Shujing Xu, Nicholas Mancuso, Paul J. Newcombe, David V. Conti (2020). "A Hierarchical Approach Using Marginal Summary Statistics for Multiple Intermediates in a Mendelian Randomization or Transcriptome Analysis." <bioRxiv><doi:10.1101/2020.02.03.924241>.

Authors:Lai Jiang <[email protected]>

hJAM_1.0.1.tar.gz
hJAM_1.0.1.zip(r-4.7)hJAM_1.0.1.zip(r-4.6)hJAM_1.0.1.zip(r-4.5)
hJAM_1.0.1.tgz(r-4.6-any)hJAM_1.0.1.tgz(r-4.5-any)
hJAM_1.0.1.tar.gz(r-4.7-any)hJAM_1.0.1.tar.gz(r-4.6-any)
hJAM_1.0.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
hJAM/json (API)

# Install 'hJAM' in R:

install.packages('hJAM', repos = c('https://uscbiostats.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/uscbiostats/hjam/issues

Datasets:

GTEx.PrCa.Amatrix - Real data for selecting the genes on chromosome 10 for the risk of prostate cancer
GTEx.PrCa.betas.gwas - Real data for selecting the genes on chromosome 10 for the risk of prostate cancer
GTEx.PrCa.betas.se.gwas - Real data for selecting the genes on chromosome 10 for the risk of prostate cancer
GTEx.PrCa.Geno - Real data for selecting the genes on chromosome 10 for the risk of prostate cancer
GTEx.PrCa.inclusion.indicator - Real data for selecting the genes on chromosome 10 for the risk of prostate cancer
GTEx.PrCa.IVWmarginal.A - Real data for selecting the genes on chromosome 10 for the risk of prostate cancer
GTEx.PrCa.maf.gwas - Real data for selecting the genes on chromosome 10 for the risk of prostate cancer
GTEx.PrCa.marginal.A - Real data for selecting the genes on chromosome 10 for the risk of prostate cancer
GTEx.PrCa.marginal.A.se - Real data for selecting the genes on chromosome 10 for the risk of prostate cancer
GTEx.PrCa.pvalues.gwas - Real data for selecting the genes on chromosome 10 for the risk of prostate cancer
MI.Amatrix - Example data of hJAM
MI.betas.gwas - Example data of hJAM
MI.Geno - Example data of hJAM
MI.marginal.Amatrix - Example data of hJAM
MI.SNPs_info - Example data of hJAM
PrCa.lipids.Amatrix - Real data for selecting the metabolites for the risk of prostate cancer
PrCa.lipids.betas.gwas - Real data for selecting the metabolites for the risk of prostate cancer
PrCa.lipids.betas.se.gwas - Real data for selecting the metabolites for the risk of prostate cancer
PrCa.lipids.Geno - Real data for selecting the metabolites for the risk of prostate cancer
PrCa.lipids.maf.gwas - Real data for selecting the metabolites for the risk of prostate cancer
PrCa.lipids.marginal.Amatrix - Real data for selecting the metabolites for the risk of prostate cancer
PrCa.lipids.pvalue.gwas - Real data for selecting the metabolites for the risk of prostate cancer
PrCa.lipids.rsid - Real data for selecting the metabolites for the risk of prostate cancer
Simulation.Amatrix - Simulation data for EN-hJAM
Simulation.betas.gwas - Simulation data for EN-hJAM
Simulation.betas.se.gwas - Simulation data for EN-hJAM
Simulation.Geno - Simulation data for EN-hJAM
Simulation.maf.gwas - Simulation data for EN-hJAM

On CRAN:

5.22 score 11 stars 8 scripts 181 downloads 14 exports 49 dependencies

Last updated from:a15efa0fcc. Checks:7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	NOTE	156
source / vignettes	OK	240
linux-release-x86_64	NOTE	200
macos-release-arm64	NOTE	121
macos-oldrel-arm64	NOTE	142
windows-devel	NOTE	144
windows-release	NOTE	123
windows-oldrel	NOTE	141
wasm-release	OK	123

Exports:EN.hJAM hJAM hJAM_egger JAM_A JAM_alphas mJAM_Forward mJAM_SuSiE mJAM_SuSiE_get_cs output.format SHAJAM SNPs_heatmap SNPs_scatter_plot susieJAM_A susieJAM_alphas

Dependencies:cli codetools cpp11 crayon dplyr farver foreach generics ggplot2 glmnet glue gmp gtable irlba isoband iterators labeling lattice lifecycle magrittr Matrix matrixcalc matrixStats mixsqp pillar pkgconfig plyr R6 RColorBrewer Rcpp RcppArmadillo RcppEigen reshape reshape2 rlang Rmpfr S7 scales shape stringi stringr survival susieR tibble tidyselect utf8 vctrs viridisLite withr

hJAM Vignette

Overview | Implementation | General input | Get conditional $\hat{A}$ matrix | Example | Data exploration | Conversion of $\hat{A}$ matrix | hJAM | Conclusion

Rendered fromhJAM_vignette.Rmdusingknitr::rmarkdown

Last update: 2021-01-06
Started: 2020-01-30

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Elastic net hJAM	EN.hJAM
Simulation data for EN-hJAM	ENhJAM.SimulationSet Simulation.Amatrix Simulation.betas.gwas Simulation.betas.se.gwas Simulation.Geno Simulation.maf.gwas
Get transformed statistics: XtX	get_XtX
Get transformed statistics: yty	get_yty
Get transformed statistics: z, or Xty	get_z
Real data for selecting the genes on chromosome 10 for the risk of prostate cancer	GTEx.PrCa GTEx.PrCa.Amatrix GTEx.PrCa.betas.gwas GTEx.PrCa.betas.se.gwas GTEx.PrCa.Geno GTEx.PrCa.inclusion.indicator GTEx.PrCa.IVWmarginal.A GTEx.PrCa.maf.gwas GTEx.PrCa.marginal.A GTEx.PrCa.marginal.A.se GTEx.PrCa.marginal.selected GTEx.PrCa.pvalues.gwas GTEx.PrCa.rsid
hJAM Fit hJAM with linear regression	hJAM
hJAM_egger Fit hJAM with Egger regression	hJAM_egger
Compute conditional A matrix	JAM_A
Compute conditional alphas	JAM_alphas
Transform log odds ratios to linear effects	LogisticToLinearEffects
Example data of hJAM	MI MI.Amatrix MI.betas.gwas MI.Geno MI.marginal.Amatrix MI.SNPs_info
Construct mJAM credible set based for selected index SNP	mJAM_build_CS
Run mJAM with Forward Selection	mJAM_Forward
Get conditional p-value under mJAM model	mJAM_get_condp
Get conditional p-value for selected (index SNPs) under mJAM model	mJAM_get_condp_selected
Get Pr(Model) based on BF-type model probability	mJAM_get_PrM
Get Pr(Model) based on Wald-type model probability	mJAM_get_PrM_Wald
Get Pr(Mediation) based on causal mediation models	mJAM_get_PrMed
Pruning SNPs based on LD	mJAM_LDpruning
Run mJAM with SuSiE	mJAM_SuSiE
Get and tidy SuSiE credible sets	mJAM_SuSiE_get_cs
Keep the output as three digits	output.format
Real data for selecting the metabolites for the risk of prostate cancer	PrCa.lipids PrCa.lipids.Amatrix PrCa.lipids.betas.gwas PrCa.lipids.betas.se.gwas PrCa.lipids.Geno PrCa.lipids.maf.gwas PrCa.lipids.marginal.Amatrix PrCa.lipids.pvalue.gwas PrCa.lipids.rsid
Print out for EN-hJAM	print.ENhJAM
Print out for hJAM	print.hJAM
Print out for hJAM_egger	print.hJAM_egger
Print out for SHA-JAM	print.SHAJAM
SHA-JAM Fit SHA-JAM	SHAJAM
Heatmap for all the SNPs used in the analysis	SNPs_heatmap
Scatter plot for SNPs vs. one intermediate in the analysis	SNPs_scatter_plot
Get SuSiE posterior mean	susie_get_posterior_mean_v2
Get SuSiE posterior sd	susie_get_posterior_sd_v2
Compute conditional A using SuSiE JAM	susieJAM_A
Compute conditional alphas using SuSiE JAM	susieJAM_alphas