Imports: sandwich, lmtest, splitstackshape, stats, parallel, abind

Suggests: glmnet, ranger, rpart, e1071, xgboost, kknn, DiceKriging,

Title: Identify Favorable Subsets of Germplasm Collections
Author: Ryan C. Graebner and Alfonso Cuesta-Marcos
Maintainer: Ryan C. Graebner <ryan.graebner@gmail.com>
Description: Finds subsets of sets of genotypes with a high mean Polymorphism Information Content (PIC), and Mean of Transformed Kinships (MTK), measures that can indicate a subset would be beneficial for rare-trait discovery and genome-wide association scanning, respectively.

Description: Finds subsets of sets of genotypes with a high Heterozygosity, and Mean of Transformed Kinships (MTK), measures that can indicate a subset would be beneficial for rare-trait discovery and genome-wide association scanning, respectively.

Title: Collection of Genetic Data Analysis Tools.
Description: GeneticTools is a loose collection of tools for the
analysis of expression and genotype data.

Description: GeneticTools is a loose collection of tools for the analysis of expression and genotype data, currently with main focus on eQTL analysis.

analysis of expression and genotype data, currently with main

Title: Collection of Genetic Data Analysis Tools
Description: A loose collection of tools for the analysis of gene expression and genotype data, currently with main focus on eQTL and MDR analysis.

Description: GeneticTools is a loose collection of tools for the analysis of expression and genotype data, currently with main focus on eQTL and MDR analysis.

Title: A Genome-Wide Scan Statistic Framework for Whole-Genome Sequence
Description: Functions for whole-genome sequencing studies, including genome-wide scan, candidate region scan and single window test.
Depends: R(>= 2.10.0), SKAT, Matrix, MASS, seqminer, data.table

Title: Detecting Signatures of Local Adaptation Based on Ancestry
Description: Portable, scalable and highly computationally efficient tool for detecting signatures of local adaptation based on multidimensional ancestry map ( _n_ X _n_ ancestry genetic trajectories, _n_ is the number of individuals). If n samples are included in the analysis, there will be n dimensional spaces that represent the common ancestry maps based on the identity-by-descent (IBD). The package calculates the correlations of loci with the common ancestry genetic maps adopting the Genomic Data Structure (GDS, Zheng et al., 2012) <doi:10.1093/bioinformatics/bts606> and suitable for millions of SNP data. Loci sharing a greater level of most recent common ancestor (MRCA) (large Z-scores) indicates a large number of individuals descend from recent common ancestors,
which signals the rapid increase in frequency of a beneficial allele due to recent positive selection. The rationale underlying this package is somewhat analogous to KLFDAPT (Qin, 2021) <doi:10.1101/2021.05.15.444294> (<https://xinghuq.github.io/KLFDAPC/articles/Genome_scan_KLFDAPC.html>). It combines the concept of IBD-based genome scan (Albrechtsen et al., 2010) <doi:10.1534/genetics.110.113977>, iHS (Voight, 2006) <doi:10.1371/journal.pbio.0040072>,
and eigenanalysis of SNP data with an identity by descent interpretation (Zheng & Weir, 2016) <doi: 10.1016/j.tpb.2015.09.004>. It can also be interpreted as spatial varying selection as ancestry genetic maps reflect geographic origins. Besides the detection of local adaptation, this package also estimates the population admixtures and plots its geographic genetic structure.
Authors@R: c(person("Xinghu", "Qin", role=c("aut", "cre", "cph"), email="qinxinghu@gmail.com", comment=c(ORCID="0000-0003-2351-3610")))
Packaged: 2021-11-11 14:06:18 UTC; Qin_st_andrews