Package: dcifer 1.5.2

Inna Gerlovina

dcifer: Genetic Relatedness Between Polyclonal Infections

An implementation of Dcifer (Distance for complex infections: fast estimation of relatedness), an identity by descent (IBD) based method to calculate genetic relatedness between polyclonal infections from biallelic and multiallelic data. The package includes functions that format and preprocess the data, implement the method, and visualize the results. Gerlovina et al. (2022) <doi:10.1093/genetics/iyac126>.

Authors:Inna Gerlovina [aut, cre]

dcifer_1.5.2.tar.gz
dcifer_1.5.2.zip(r-4.7)dcifer_1.5.2.zip(r-4.6)dcifer_1.5.2.zip(r-4.5)
dcifer_1.5.2.tgz(r-4.6-x86_64)dcifer_1.5.2.tgz(r-4.6-arm64)dcifer_1.5.2.tgz(r-4.5-x86_64)dcifer_1.5.2.tgz(r-4.5-arm64)
dcifer_1.5.2.tar.gz(r-4.7-arm64)dcifer_1.5.2.tar.gz(r-4.7-x86_64)dcifer_1.5.2.tar.gz(r-4.6-arm64)dcifer_1.5.2.tar.gz(r-4.6-x86_64)
dcifer_1.5.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
dcifer/json (API)

# Install 'dcifer' in R:

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

Bug tracker:https://github.com/eppicenter/dcifer/issues

Pkgdown/docs site:https://eppicenter.github.io

Datasets:

dres - Dcifer results
dsmp - Sample data
revals - Parameter grid

On CRAN:

5.85 score 8 stars 25 scripts 303 downloads 16 exports 0 dependencies

Last updated from:b6255509bb. Checks:13 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	OK	115
linux-devel-x86_64	OK	116
source / vignettes	OK	149
linux-release-arm64	OK	108
linux-release-x86_64	OK	134
macos-release-arm64	OK	95
macos-release-x86_64	OK	207
macos-oldrel-arm64	OK	106
macos-oldrel-x86_64	OK	143
windows-devel	OK	85
windows-release	OK	83
windows-oldrel	OK	90
wasm-release	OK	90

Exports:calcAfreq formatAfreq formatDat generateReval getCOI ibdDat ibdEstM ibdPair logReval matchAfreq mixMat plotColorbar plotRel probUxUy readAfreq readDat

Dependencies:

Dcifer: Genetic Distance Between Polyclonal Infections

Read and reformat data, estimate COI and population allele frequencies | Estimate relatedness | Visualize the results | Further analysis of related samples

Rendered fromvignetteDcifer.Rmdusingknitr::rmarkdown

Last update: 2025-11-07
Started: 2022-06-05

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Calculate Allele Frequencies	calcAfreq
Dcifer results	dres
Sample data	dsmp
Read and Reformat Data	format formatAfreq formatDat readAfreq readDat
Grid of Parameter Values	generateReval
Calculate COI	getCOI
Pairwise Relatedness	ibdDat
Estimate Relatedness and a Number of Related Strains	ibdEstM
Relatedness Between Two Samples	ibdPair
Logarithms of 'reval'	logReval
Match Samples and Allele Frequencies	matchAfreq
Combine two matrices	mixMat
Colorbar	plotColorbar
Plot Relatedness Estimates	plotRel
Likelihood for U_x, U_y	probUxUy
Parameter grid	revals