imputeqc is an R package and accompanied scripts to estimate the quality of imputation of genotypes that was made with fastPHASE tool. It allows to choose the appropriate number of haplotype clusters (K) for the search of selection fingerprints with hapFLK test.
- Make sure you have devtools package installed. Run from R
install.packages("devtools")
- Install imputeqc
devtools::install_github("inzilico/imputeqc", build_vignettes = TRUE)
Read a vignette How to Select the Number of Clusters for fastPHASE:
- download *.pdf.
- 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")
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.