Package: BREADR 1.0.2.9000

BREADR: Estimates Degrees of Relatedness (Up to the Second Degree) for Extreme Low-Coverage Data

The goal of the package is to provide an easy-to-use method for estimating degrees of relatedness (up to the second degree) for extreme low-coverage data. The package also allows users to quantify and visualise the level of confidence in the estimated degrees of relatedness.

Authors:Jono Tuke [aut, cre], Adam B. Rohrlach [aut], Wolfgang Haak [aut], Divyaratan Popli [aut]

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BREADR.pdf |BREADR.html✨
BREADR/json (API)
NEWS

# Install 'BREADR' in R:

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

Bug tracker:https://github.com/jonotuke/breadr/issues

Datasets:

counts_example - Counts_example
relatedness_example - Relatedness_example

On CRAN:

4.30 score 8 stars 4 scripts 345 downloads 13 exports 81 dependencies

Last updated 3 months agofrom:47afeeec59. Checks:OK: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 08 2024
R-4.5-win	OK	Nov 08 2024
R-4.5-linux	OK	Nov 08 2024
R-4.4-win	OK	Nov 08 2024
R-4.4-mac	OK	Nov 08 2024
R-4.3-win	OK	Nov 08 2024
R-4.3-mac	OK	Nov 08 2024

Exports:%>%callRelatedness get_column_new plotLOAF plotSLICE processEigenstrat processEigenstrat_old read_ind read_snp saveSLICES sim_geno split_line test_degree

Dependencies:abind backports bit bit64 boot broom car carData cli clipr colorspace corrplot cowplot cpp11 crayon data.table Deriv doBy dplyr fansi farver forcats Formula generics ggplot2 ggpubr ggrepel ggsci ggsignif glue gridExtra gtable hms isoband labeling lattice lifecycle lme4 magrittr MASS Matrix MatrixModels matrixStats mgcv microbenchmark minqa modelr munsell nlme nloptr nnet numDeriv pbkrtest pillar pkgconfig polynom prettyunits progress purrr quantreg R6 RColorBrewer Rcpp RcppEigen readr rlang rstatix scales SparseM stringi stringr survival tibble tidyr tidyselect tzdb utf8 vctrs viridisLite vroom withr

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
callRelatedness	callRelatedness
counts_example	counts_example
get column	get_column_new
plotLOAF	plotLOAF
plotSLICE	plotSLICE
process Eigenstrat data - alternative version	processEigenstrat
process Eigenstrat data	processEigenstrat_old
read_ind	read_ind
read_snp	read_snp
relatedness_example	relatedness_example
saveSLICES	saveSLICES
sim_geno	sim_geno
split line	split_line
test_degree	test_degree