Package: gwid 0.3.0

Soroush Mahmoudiandehkordi

gwid: Genome-Wide Identity-by-Descent

Methods and tools for the analysis of Genome Wide Identity-by-Descent ('gwid') mapping data, focusing on testing whether there is a higher occurrence of Identity-By-Descent (IBD) segments around potential causal variants in cases compared to controls, which is crucial for identifying rare variants. To enhance its analytical power, 'gwid' incorporates a Sliding Window Approach, allowing for the detection and analysis of signals from multiple Single Nucleotide Polymorphisms (SNPs).

Authors:Soroush Mahmoudiandehkordi [aut, cre], Steven J Schrodi [aut], Mehdi Maadooliat [aut]

gwid_0.3.0.tar.gz
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gwid.pdf |gwid.html✨
gwid/json (API)
NEWS

# Install 'gwid' in R:

install.packages('gwid', repos = c('https://soroushmdg.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/soroushmdg/gwid/issues

Pkgdown site:https://soroushmdg.github.io

On CRAN:

3.60 score 1 stars 4 scripts 316 downloads 17 exports 86 dependencies

Last updated 7 months agofrom:e419647170. Checks:6 OK, 3 NOTE. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Mar 08 2025
R-4.5-win	NOTE	Mar 08 2025
R-4.5-mac	NOTE	Mar 08 2025
R-4.5-linux	NOTE	Mar 08 2025
R-4.4-win	OK	Mar 08 2025
R-4.4-mac	OK	Mar 08 2025
R-4.4-linux	OK	Mar 08 2025
R-4.3-win	OK	Mar 08 2025
R-4.3-mac	OK	Mar 08 2025

Exports:build_gwas build_gwid build_phase case_control extract extract_window fisher_test gtest haplotype_frequency haplotype_structure launch_app mcnemar_test mcnemar_test_permut permutation_test print roh subset

Dependencies:askpass base64enc bslib cachem cli colorspace commonmark cpp11 crayon crosstalk curl data.table digest dplyr evaluate fansi farver fastmap fontawesome fs gdsfmt generics ggplot2 gh gitcreds glue gtable highr htmltools htmlwidgets httpuv httr httr2 ini isoband jquerylib jsonlite knitr labeling later lattice lazyeval lifecycle lubridate magrittr MASS Matrix memoise mgcv mime munsell nlme openssl piggyback pillar pkgconfig plotly promises purrr R6 rappdirs RColorBrewer Rcpp RcppRoll rlang rmarkdown sass scales shiny SNPRelate sourcetools stringi stringr sys tibble tidyr tidyselect timechange tinytex utf8 vctrs viridisLite withr xfun xtable yaml

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Open a SNP GDS file and extract information.	build_gwas
Open a ibd file and extract information.	build_gwid
Read .vcf structured text format files and reduce the size of file.	build_phase
Reload saved case-control list file	case_control
Extract information from SNP GDS file.	extract
extract component of an object	extract_window
Extract information from ibd data in a moving window	extract_window.gwid
Extract information from SNP GDS file.	extract.gwas
Extract information from ibd data.	extract.gwid
Fisher test	fisher_test
Fisher's Exact Test for gwas count data	fisher_test.gwas
Fisher's Exact Test for gwid count data	fisher_test.gwid
fisher exact test for result_snps count data	fisher_test.result_snps
perform gtest	gtest
Perform G-test on haplotype structures extracted from 'haplotype_structure' function	gtest.haplotype_structure
haplotype frequency	haplotype_frequency
haplotype frequency in sliding windows	haplotype_frequency.haplotype_structure
haplotype structures in a window	haplotype_structure
extract haplotype structures of individuals in a window	haplotype_structure.gwas
extract haplotype structures of pairwise ibd samples in a window	haplotype_structure.gwid
laucnh a shiny app	launch_app
mcnemar test	mcnemar_test
mcnemar permutation	mcnemar_test_permut
mcnemar permutation test	mcnemar_test_permut.result_snps
mcnemar test	mcnemar_test.result_snps
permutation test	permutation_test
Permutation test for gwas object	permutation_test.gwas
permutation test for gwid count data	permutation_test.gwid
Permutation test for `haplotype_structure` object	permutation_test.haplotype_structure
Line plot of gwas objects	plot.gwas
Line plot of gwid objects	plot.gwid
Line plot of haplotype_frequency object	plot.haplotype_frequency
Two type of line plots for haplotype_structure_frequency objects .	plot.haplotype_structure_frequency
Line plot of result_snps objects	plot.result_snps
Line plot of test_snps objects	plot.test_snps
print	print
print gwas instants	print.gwas
runs of homozygosity	roh
runs of homozygosity	roh.phase
subset an object	subset
subset gwid object based on snp position	subset.gwid