Package: neutralitytestr 0.0.3

neutralitytestr: Test for a Neutral Evolutionary Model in Cancer Sequencing Data

Package takes frequencies of mutations as reported by high throughput sequencing data from cancer and fits a theoretical neutral model of tumour evolution. Package outputs summary statistics and contains code for plotting the data and model fits. See Williams et al 2016 <doi:10.1038/ng.3489> and Williams et al 2017 <doi:10.1101/096305> for further details of the method.

Authors:Marc Williams [aut, cre]

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

# Install 'neutralitytestr' in R:

install.packages('neutralitytestr', repos = c('https://marcjwilliams1.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/marcjwilliams1/neutralitytestr/issues

Datasets:

VAFneutral - Synthetic sequencing data generated from a evolutionary based cancer simulation.
VAFselection - Synthetic sequencing data generated from a evolutionary based cancer simulation.

On CRAN:

5.10 score 10 stars 25 scripts 158 downloads 5 exports 60 dependencies

Last updated 4 years agofrom:86911335a5. Checks:OK: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 01 2024
R-4.5-win	OK	Nov 01 2024
R-4.5-linux	OK	Nov 01 2024
R-4.4-win	OK	Nov 01 2024
R-4.4-mac	OK	Nov 01 2024
R-4.3-win	OK	Nov 01 2024
R-4.3-mac	OK	Nov 01 2024

Exports:lsq_plot neutralitytest normalized_plot plot_all vaf_histogram

Dependencies:boot cli codetools colorspace confintr cowplot cpp11 dplyr fansi farver generics ggplot2 ggpmisc ggpp glue gridExtra gtable isoband labeling lattice lifecycle lmodel2 lubridate magrittr MASS Matrix MatrixModels mgcv multcomp multcompView munsell mvtnorm nlme pillar pkgconfig plyr polynom pracma quantreg R6 RColorBrewer Rcpp rlang sandwich scales SparseM splus2R stringi stringr survival TH.data tibble tidyselect timechange utf8 vctrs viridisLite withr xts zoo

neutralitytestr: Testing a neutral evolutionary model on cancer sequencing data

Marc Williams

Rendered fromneutraltytestr.Rmdusingknitr::rmarkdownon Nov 01 2024.

Last update: 2018-05-21
Started: 2018-04-09

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Plot cumulative distribution 'lsq_plot' Plots the cumulative distribution of the data as well as the best fit linear model line.	lsq_plot
Testing for neutrality on cancer sequencing data	neutralitytest
'neutralitytestr' package	neutralitytestr
Plot normalized cumulative distribution 'normalized_plot' Plots the (normalized) cumulative distribution of the data as well as the theoretical expectation from a neutral evolutionary model.	normalized_plot
Plot all plots in the package and make composite figure. 'plot_all' Plots histogram, linear model best fit plot and normalized plot and plot and makes composite figure.	plot_all
Plot VAF histogram 'vaf_histogram' Plots a histogram of the variant allele frequencies.	vaf_histogram
Synthetic sequencing data generated from a evolutionary based cancer simulation.	VAFneutral
Synthetic sequencing data generated from a evolutionary based cancer simulation.	VAFselection