LocStra: Fast analysis of regional/global stratification in whole-genome sequencing studies.

ABSTRACT: locStra is an R -package for the analysis of regional and global population stratification in whole-genome sequencing (WGS) studies, where regional stratification refers to the substructure defined by the loci in a particular region on the genome. Population substructure can be assessed based on the genetic covariance matrix, the genomic relationship matrix, and the unweighted/weighted genetic Jaccard similarity matrix. Using a sliding window approach, the regional similarity matrices are compared with the global ones, based on user-defined window sizes and metrics, for example, the correlation between regional and global eigenvectors. An algorithm for the specification of the window size is provided. As the implementation fully exploits sparse matrix algebra and is written in C++, the ana

SUBMITTER: Hahn G 

PROVIDER: S-EPMC7856019 | biostudies-literature | 2021 Feb

REPOSITORIES: biostudies-literature