Overview | Installation | Required files | Allele reference panels | The header-translation table | Configuration file | Step-by-step guide to run a QC | Step 1: make sure the package is installed correctly | Step 2: check R environment | Step 3: download the standard allele-frequency reference datasets | Step 4: get the header-translation table | Step 5: get the configuration file | Step 6: modify the parameters in the configuration file | Step 7: run the QC function | Test run
Package: GWASinspector 1.7.4
Alireza Ani
GWASinspector: Comprehensive and Easy to Use Quality Control of GWAS Results
When evaluating the results of a genome-wide association study (GWAS), it is important to perform a quality control to ensure that the results are valid, complete, correctly formatted, and, in case of meta-analysis, consistent with other studies that have applied the same analysis. This package was developed to facilitate and streamline this process and provide the user with a comprehensive report.
Authors:
GWASinspector_1.7.4.tar.gz
GWASinspector_1.7.4.tar.gz(r-4.7-any)GWASinspector_1.7.4.tar.gz(r-4.6-any)
GWASinspector_1.7.4.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
GWASinspector/json (API)
| # Install 'GWASinspector' in R: |
| install.packages('GWASinspector', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated from:78fe337483. Checks:4 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 176 | ||
| source / vignettes | OK | 194 | ||
| linux-release-x86_64 | OK | 173 | ||
| wasm-release | OK | 180 |
Exports:compare_GWASsdemo_inspectorget_configget_headerTranslationmanhattan_plotresult_inspectorrun_inspectorsetup_inspectorsystem_check
Dependencies:base64encbitbit64blobbslibcachemclicpp11data.tableDBIdigestevaluatefarverfastmapfontawesomefsggplot2gluegridExtragtablehashhighrhtmltoolsiniisobandjquerylibjsonlitekableExtraknitrlabelinglifecycleloggermagrittrmemoisemimeopenxlsxpkgconfigR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcpprlangrmarkdownRSQLiterstudioapiS7sassscalesstringistringrsvglitesystemfontstextshapingtinytexvctrsviridisLitewithrxfunxml2yamlzip
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Compare summary statistics of GWAS result files | compare_GWASs |
| Runs an example QC | demo_inspector |
| Copies the template configuration file to the local machine | get_config |
| Copies the template header translation table to the local machine | get_headerTranslation |
| Comprehensive and Easy to Use Quality Control of GWAS Results | GWASinspector-package GWASinspector |
| An S4 class to represent the methods and parameters for inspecting a list of GWAS study result files. | Inspector Inspector-class |
| Creates the Manhattan plot | manhattan_plot |
| Displays a brief report after running the QC pipeline | result_inspector |
| Runs the QC pipeline on a set of GWAS result files | run_inspector |
| Importing a configuration file into R for setting the pipeline parameters | setup_inspector |
| An S4 class to represent an inspected GWAS study result file. | Study Study-class |
| An S4 class to represent a list of inspected GWAS study result files. | StudyList StudyList-class |
| Checks which required and optional packages are available | system_check |