1 Introduction | 2 Loading Data | 3 Preparation of Standard Beta Table | 4 Two-way Scatter Plots for Beta Values of Disease and Undefined Causal Variables | 5 MR and Path Analysis | 6 Create Path Diagram | 7 Create Two-level Nested Path Diagram | 8 SNP Annotation Analysis | 9 Session Info
Package: GMRP 1.41.0
Yuan-De Tan
GMRP: GWAS-based Mendelian Randomization and Path Analyses
Perform Mendelian randomization analysis of multiple SNPs to determine risk factors causing disease of study and to exclude confounding variabels and perform path analysis to construct path of risk factors to the disease.
Authors:
GMRP_1.41.0.tar.gz
GMRP_1.41.0.zip(r-4.7)GMRP_1.41.0.zip(r-4.6)GMRP_1.41.0.zip(r-4.5)
GMRP_1.41.0.tgz(r-4.6-any)GMRP_1.41.0.tgz(r-4.5-any)
GMRP_1.41.0.tar.gz(r-4.7-any)GMRP_1.41.0.tar.gz(r-4.6-any)
GMRP_1.41.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
GMRP/json (API)
| # Install 'GMRP' in R: |
| install.packages('GMRP', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- beta.data - Beta Data Of SNP Regressed on Causal Variables and Disease
- cad.data - BoldGWAS Meta-analyzed Data of Coronary Artery Disease
- lpd.data - *GWAS* Meta-analyzed Data of Lipoprotein Cholesterols
- SNP358.data - Data of 358 SNPs
- SNP368annot.data - Annotation data of 368SNPs
On BioConductor:GMRP-1.41.0(bioc 3.24)GMRP-1.40.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated from:a31ee7640e. Checks:1 ERROR, 4 NOTE, 2 OK, 3 WARNING. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 175 | ||
| linux-devel-x86_64 | NOTE | 176 | ||
| source / vignettes | OK | 186 | ||
| linux-release-x86_64 | NOTE | 210 | ||
| macos-release-arm64 | NOTE | 121 | ||
| macos-oldrel-arm64 | NOTE | 107 | ||
| windows-devel | WARNING | 113 | ||
| windows-release | WARNING | 106 | ||
| windows-oldrel | WARNING | 100 | ||
| wasm-release | OK | 122 |
Exports:chrpfmergemktablepathpathdiagrampathdiagram2snpPositAnnotucscannot
Dependencies:BiocGenericsdiagramgenericsGenomicRangesIRangesplotrixS4VectorsSeqinfoshape
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| *GWAS*-based Mendelian Randomization Path Analysis | GMRP-package GMRP |
| Beta Data Of SNP Regressed on Causal Variables and Disease | beta.data |
| boldGWAS Meta-analyzed Data of Coronary Artery Disease | cad.data |
| Split hg19 | chrp |
| Merge Two *GWAS* Result Data Sheets | fmerge |
| *GWAS* Meta-analyzed Data of Lipoprotein Cholesterols | lpd.data |
| Selection of SNPs and Creation of A Standard Table for Mendelian Randomization and Path Analyses | mktable |
| Path Analysis | path |
| Path Diagram | pathdiagram |
| Two-level Nested Pathdiagram | pathdiagram2 |
| Data of 358 SNPs | SNP358.data |
| Annotation data of 368SNPs | SNP368annot.data |
| _SNP_ Position Annotation | snpPositAnnot |
| Functional Annotation of _SNP_s Chosen | ucscannot |
