SNPfiltR

1.0.7

Interactively Filter SNP Datasets

0packages depend

12.2Kdownloads / year

84.5%test coverage

13/13checks pass

Overview

About

Maintained by Devon DeRaadFirst published 2021-10-285 releasesCRAN page ↗

Is designed to interactively and reproducibly visualize and filter SNP (single-nucleotide polymorphism) datasets. This R-based implementation of SNP and genotype filters facilitates an interactive and iterative SNP filtering pipeline, which can be documented reproducibly via 'rmarkdown'. 'SNPfiltR' contains functions for visualizing various quality and missing data metrics for a SNP dataset, and then filtering the dataset based on user specified cutoffs. All functions take 'vcfR' objects as input, which can easily be generated by reading standard vcf (variant call format) files into R using the R package 'vcfR' authored by Knaus and Grünwald (2017) doi:10.1111/1755-0998.12549. Each 'SNPfiltR' function can return a newly filtered 'vcfR' object, which can then be written to a local directory in standard vcf format using the 'vcfR' package, for downstream population genetic and phylogenetic analyses.

Install

R (CRAN)Ubuntu (r2u)Fedora (COPR)

install.packages("SNPfiltR", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-snpfiltr

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-SNPfiltR

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

Health

CRAN checks

13OK

Slowest check: 2.4 min · r-release-windows-x86_64

Code health

Yes

Tests · ratio 0.22

84.5%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 2,060 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

12.2K

CRAN downloads in the past year

Rank #6,039 · ~33/day · ~1K/mo

Releases R versions

Daily download trend is not available in this view yet.

31630 days

1.5K90 days

12.2K1 year

Compare downloads with other packages →

Also on108 r2u35 c2d4u

Dependencies

Declared dependencies

8 external dependencies (excludes base and recommended)

Depends (1)

R >= 2.10

Imports (10)

vcfR ggplot2 Rtsneclusteradegenet gridExtra ggridgesstatsgraphicsutils

LinkingTo (0)

none

Suggests (2)

rmarkdown knitr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (1)

Maintainer (1)

Devon DeRaad

Author, Maintainer

Authors (1)

Devon DeRaad

Author, Maintainer

Package Timeline

5 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
1.0.7Latest
2025-09-04 · current release · diff ↗
unarchivedReturned to CRAN
2025-09-04
R
R 4.5.0 released · 2025-04-11
archivedRemoved from CRAN
2025-01-11
issues were not corrected in time
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
1.0.1
2023-03-17 · diff ↗
R
R 4.2.0 released · 2022-04-22
1.0.0
2022-04-16 · diff ↗
0.1.1
2022-01-25 · diff ↗
unarchivedReturned to CRAN
2022-01-25
archivedRemoved from CRAN
2022-01-06
check issues were not corrected in time
0.1.0
2021-10-28
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2021-10-28
Total releases: 5 / 5 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 2.10
Bundled data: 47 KB / 2 files
Download size: 627 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Report a problem with this page →