Authors@R: c( person(given = "Victor", family = "Moreno", role = "aut"),
person(given = "Juan R", family = "Gonzalez", email = "juanr.gonzalez@isglobal.org", role = c("aut")),
person(given = "Dolors", family = "Pelegri", email = "dolors.pelegri@isglobal.org", role = c("aut", "cre")))

Suggests: testthat, knitr, rmarkdown, biomaRt, VariantAnnotation,
person(given = "Juan R", family = "Gonzalez",
email = "juanr.gonzalez@isglobal.org", role = c("aut")),
person(given = "Dolors", family = "Pelegri",
email = "dolors.pelegri@isglobal.org", role = c("aut", "cre")))
Description: Functions to perform most of the common analysis in genome
association studies are implemented. These analyses include descriptive
statistics and exploratory analysis of missing values, calculation of
Hardy-Weinberg equilibrium, analysis of association based on generalized
linear models (either for quantitative or binary traits), and analysis
of multiple SNPs (haplotype and epistasis analysis). Permutation test
and related tests (sum statistic and truncated product) are also
implemented. Max-statistic and genetic risk-allele score exact
distributions are also possible to be estimated. The methods are
described in Gonzalez JR et al., 2007 <doi: 10.1093/bioinformatics/btm025>.

Packaged: 2020-11-10 19:32:05 UTC; jrgonzalez

Title: Interactively Filter SNP Datasets
Description: Is designed to interactively and reproducibly visualize and filter SNP
(single-nucleotide polymorphism) datasets. This R-based implementation of SNP
an interactive and iterative SNP filtering pipeline, which can be documented
reproducibly via Rmarkdown. 'SNPfiltR' contains functions for visualizing
various quality and missing data metrics for a SNP dataset, and then filtering
the dataset based on user specified cutoffs.
All functions take 'vcfR' objects as input, which can easily be
generated by reading standard vcf (variant call format) files into R using
the R package 'vcfR' (Knaus and Grünwald) (<doi:10.1111/1755-0998.12549>).
Each 'SNPfiltR' function can return a newly filtered vcfR object, which can then be
written to a local directory in standard vcf format using the 'vcfR' package,
for downstream population genetic and phylogenetic analyses.
Imports: vcfR, ggplot2, Rtsne, cluster, adegenet, gridExtra, ggridges,