Kernel Local Fisher Discriminant Analysis of Principal Components (KLFDAPC) for large genomic data

Install packages

Install the most recent version of the KLFDAPC package using devtools:

library("devtools")

devtools::install_github("xinghuq/KLFDAPC")

Alternatively, you can install from the source files, run the following commands in the shell:

R CMD build KLFDAPC
R CMD check --as-cran KLFDAPC_0.1.0.tar.gz
R CMD INSTALL KLFDAPC_0.1.0.tar.gz

Dependencies

Before install or during installation, make sure the below dependences are installed.

requireNamespace("SNPRelate")

if (!requireNamespace("BiocManager", quietly=TRUE))

  install.packages("BiocManager",repos = "http://cran.us.r-project.org")
  
if (!requireNamespace("SNPRelate", quietly=TRUE))

  BiocManager::install("SNPRelate")
  
 if (!requireNamespace("DA", quietly=TRUE))
 
  devtools::install_github("xinghuq/DA")

Vignettes and tutorials

vignette("Population_structure_of_Covid")

vignette("Population_structure_of_RegMap")

vignette("Genome_scan_KLFDAPC")

Welcome any feedback and pull request.

Citation

Qin. X. 2020. KLFDAPC: Kernel local Fisher discriminant analysis of principal components (KLFDAPC) for large genomic data. R package version 0.2.0.

Qin, X., Chiang, C.W.K., and Gaggiotti, O.E. (2022). [KLFDAPC: A Supervised Machine Learning Approach for Spatial Genetic Structure Analysis](10.1093/bib/bbac202). Briefings in Bioinformatics, 10.1093/bib/bbac202.