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-4.5)hJAM_1.0.1.zip(r-4.4)hJAM_1.0.1.zip(r-4.3)
hJAM_1.0.1.tgz(r-4.4-any)hJAM_1.0.1.tgz(r-4.3-any)
hJAM_1.0.1.tar.gz(r-4.5-noble)hJAM_1.0.1.tar.gz(r-4.4-noble)
hJAM_1.0.1.tgz(r-4.4-emscripten)hJAM_1.0.1.tgz(r-4.3-emscripten)
hJAM.pdf |hJAM.html✨
hJAM/json (API)

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

Peer review:

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

Datasets:

On CRAN:

5.61 score 9 stars 5 scripts 133 downloads 14 exports 53 dependencies

Last updated 10 months agofrom:a15efa0fcc. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 14 2024
R-4.5-winNOTENov 14 2024
R-4.5-linuxNOTENov 14 2024
R-4.4-winNOTENov 14 2024
R-4.4-macNOTENov 14 2024
R-4.3-winNOTENov 14 2024
R-4.3-macNOTENov 14 2024

Exports:EN.hJAMhJAMhJAM_eggerJAM_AJAM_alphasmJAM_ForwardmJAM_SuSiEmJAM_SuSiE_get_csoutput.formatSHAJAMSNPs_heatmapSNPs_scatter_plotsusieJAM_AsusieJAM_alphas

Dependencies:clicodetoolscolorspacecrayondplyrfansifarverforeachgenericsggplot2glmnetgluegmpgtableirlbaisobanditeratorslabelinglatticelifecyclemagrittrMASSMatrixmatrixcalcmatrixStatsmgcvmixsqpmunsellnlmepillarpkgconfigplyrR6RColorBrewerRcppRcppArmadilloRcppEigenreshapereshape2rlangRmpfrscalesshapestringistringrsurvivalsusieRtibbletidyselectutf8vctrsviridisLitewithr

hJAM Vignette

Lai Jiang

Rendered fromhJAM_vignette.Rmdusingknitr::rmarkdownon Nov 14 2024.

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

Readme and manuals

Help Manual

Help pageTopics
Elastic net hJAMEN.hJAM
Simulation data for EN-hJAMENhJAM.SimulationSet Simulation.Amatrix Simulation.betas.gwas Simulation.betas.se.gwas Simulation.Geno Simulation.maf.gwas
Get transformed statistics: XtXget_XtX
Get transformed statistics: ytyget_yty
Get transformed statistics: z, or Xtyget_z
Real data for selecting the genes on chromosome 10 for the risk of prostate cancerGTEx.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 regressionhJAM
hJAM_egger Fit hJAM with Egger regressionhJAM_egger
Compute conditional A matrixJAM_A
Compute conditional alphasJAM_alphas
Transform log odds ratios to linear effectsLogisticToLinearEffects
Example data of hJAMMI MI.Amatrix MI.betas.gwas MI.Geno MI.marginal.Amatrix MI.SNPs_info
Construct mJAM credible set based for selected index SNPmJAM_build_CS
Run mJAM with Forward SelectionmJAM_Forward
Get conditional p-value under mJAM modelmJAM_get_condp
Get conditional p-value for selected (index SNPs) under mJAM modelmJAM_get_condp_selected
Get Pr(Model) based on BF-type model probabilitymJAM_get_PrM
Get Pr(Model) based on Wald-type model probabilitymJAM_get_PrM_Wald
Get Pr(Mediation) based on causal mediation modelsmJAM_get_PrMed
Pruning SNPs based on LDmJAM_LDpruning
Run mJAM with SuSiEmJAM_SuSiE
Get and tidy SuSiE credible setsmJAM_SuSiE_get_cs
Keep the output as three digitsoutput.format
Real data for selecting the metabolites for the risk of prostate cancerPrCa.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-hJAMprint.ENhJAM
Print out for hJAMprint.hJAM
Print out for hJAM_eggerprint.hJAM_egger
Print out for SHA-JAMprint.SHAJAM
SHA-JAM Fit SHA-JAMSHAJAM
Heatmap for all the SNPs used in the analysisSNPs_heatmap
Scatter plot for SNPs vs. one intermediate in the analysisSNPs_scatter_plot
Get SuSiE posterior meansusie_get_posterior_mean_v2
Get SuSiE posterior sdsusie_get_posterior_sd_v2
Compute conditional A using SuSiE JAMsusieJAM_A
Compute conditional alphas using SuSiE JAMsusieJAM_alphas