Package: zalpha 0.3.0.9999

zalpha: Run a Suite of Selection Statistics

A suite of statistics for identifying areas of the genome under selective pressure. See Jacobs, Sluckin and Kivisild (2016) <doi:10.1534/genetics.115.185900>.

Authors:Clare Horscroft

zalpha_0.3.0.9999.tar.gz
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zalpha_0.3.0.9999.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
zalpha/json (API)

# Install 'zalpha' in R:

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

Bug tracker:https://github.com/chorscroft/zalpha/issues

Datasets:

LDprofile - Dataset containing an example LD profile
snps - Dataset containing details on simulated SNPs

On CRAN:

evolution genetics

4.00 score 2 stars 5 scripts 256 downloads 16 exports 0 dependencies

Last updated from:dd6fea5dca. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	130
source / vignettes	OK	155
linux-release-x86_64	OK	118
macos-release-arm64	OK	147
macos-oldrel-arm64	OK	158
windows-devel	OK	105
windows-release	OK	96
windows-oldrel	OK	76
wasm-release	OK	108

Exports:create_LDprofile L_plus_R LR Zalpha Zalpha_all Zalpha_BetaCDF Zalpha_expected Zalpha_log_rsq_over_expected Zalpha_rsq_over_expected Zalpha_Zscore Zbeta Zbeta_BetaCDF Zbeta_expected Zbeta_log_rsq_over_expected Zbeta_rsq_over_expected Zbeta_Zscore

Dependencies:

zalpha

Rendered fromzalpha.Rmdusingknitr::rmarkdown

Last update: 2021-07-14
Started: 2020-02-24

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Creates an LD profile	create_LDprofile
Runs the L_plus_R function	L_plus_R
Dataset containing an example LD profile	LDprofile
Runs the LR function	LR
Dataset containing details on simulated SNPs	snps
Runs the Zalpha function	Zalpha
Runs all the statistics in the zalpha package	Zalpha_all
Runs the Zalpha function using a cumulative beta distribution function on the r-squared values for the region	Zalpha_BetaCDF
Runs the Zalpha function on the expected r-squared values for the region	Zalpha_expected
Runs the Zalpha function on the log of the r-squared values over the expected r-squared values for the region	Zalpha_log_rsq_over_expected
Runs the Zalpha function on the r-squared values over the expected r-squared values for the region	Zalpha_rsq_over_expected
Runs the Zalpha function using the Z score of the r-squared values for the region	Zalpha_Zscore
Runs the Zbeta function	Zbeta
Runs the Zbeta function using a cumulative beta distribution function on the r-squared values for the region	Zbeta_BetaCDF
Runs the Zbeta function on the expected r-squared values for the region	Zbeta_expected
Runs the Zbeta function on the log of the r-squared values over the expected r-squared values for the region	Zbeta_log_rsq_over_expected
Runs the Zbeta function on the r-squared values over the expected r-squared values for the region	Zbeta_rsq_over_expected
Runs the Zbeta function using the Z score of the r-squared values for the region	Zbeta_Zscore