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An R package to estimate the quality of imputation of genotypes.
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README.md

README.md

What is it

imputeqc is an R package and accompanied scripts to estimate the quality of imputation of genotypes that was made with fastPHASE and BEAGLE softwares. Any other tools that support *.inp fastPHASE or VCF files can be also considered. The package is based on masked data analysis.

Possible applications

  1. Estimation of the error of gynotype imputation.

  2. Optimization of the imputation model parameters, e.g., the number of haplotype clusters. The parameter can be further used for the search of signatures of selection with hapFLK test.

  3. Testing different reference panels for imputation.

  4. Benchmarking of different imputation softwares and strategies.

Ho to install from GitHub

Run from R.

  1. Make sure you have devtools package installed.
install.packages("devtools")
  1. Install dependencies
install.packages("BiocManager")
BiocManager::install("VariantAnnotation")
  1. Install imputeqc
devtools::install_github("inzilico/imputeqc", build_vignettes = TRUE)

How to use

Read a vignette How to Select the Number of Clusters for fastPHASE.

  • On a local machine, the vignette can be accessed as follow:
browseVignettes("imputeqc")
  • On remote machine, the vignette can be opened in the "Help" tab of RStudio:
vignette("k_selection")

License

MIT

Citing

Gennady Khvorykh. inzilico/imputeqc v1.0.0 (2018). GitHub repository, https://github.com/inzilico/imputeqc.

Contacts

Gennady Khvorykh, a bioinformatician, inzilico.com

Interested in contributing to the project? Suggestions, questions, and comments are open! Feel free to drop me the message.

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