polyRAD
Genotype Calling with Uncertainty from Sequencing Data in Polyploids and Diploids
Description
Read depth data from genotyping-by-sequencing (GBS) or restriction site-associated DNA sequencing (RAD-seq) are imported and used to make Bayesian probability estimates of genotypes in polyploids or diploids. The genotype probabilities, posterior mean genotypes, or most probable genotypes can then be exported for downstream analysis. 'polyRAD' is described by Clark et al. (2019) <doi:10.1534/g3.118.200913>, and the Hind/He statistic for marker filtering is described by Clark et al. (2022) <doi:10.1186/s12859-022-04635-9>. A variant calling pipeline for highly duplicated genomes is also included and is described by Clark et al. (2020, Version 1) <doi:10.1101/2020.01.11.902890>.
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Show all 14 flavors
| Flavor | Status |
|---|---|
| r-devel-linux-x86_64-debian-clang | OK |
| r-devel-linux-x86_64-debian-gcc | WARNING |
| r-devel-linux-x86_64-fedora-clang | WARNING |
| r-devel-linux-x86_64-fedora-gcc | WARNING |
| r-devel-macos-arm64 | OK |
| r-devel-windows-x86_64 | OK |
| r-oldrel-macos-arm64 | NOTE |
| r-oldrel-macos-x86_64 | NOTE |
| r-oldrel-windows-x86_64 | NOTE |
| r-patched-linux-x86_64 | OK |
| r-release-linux-x86_64 | OK |
| r-release-macos-arm64 | OK |
| r-release-macos-x86_64 | OK |
| r-release-windows-x86_64 | OK |
Check details (14 non-OK)
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Rd cross-references
Missing link(s) in Rd file 'LocusInfo.Rd':
‘[GenomicFeatures]{makeTxDbFromGFF}’
See section 'Cross-references' in the 'Writing R Extensions' manual.
Rd cross-references
Undeclared packages ‘polymapR’, ‘BSgenome’ in Rd xrefs
Missing link(s) in Rd file 'LocusInfo.Rd':
‘[GenomicFeatures]{makeTxDbFromGFF}’
See section 'Cross-references' in the 'Writing R Extensions' manual.
Rd cross-references
Missing link(s) in Rd file 'LocusInfo.Rd':
‘[GenomicFeatures]{makeTxDbFromGFF}’
See section 'Cross-references' in the 'Writing R Extensions' manual.
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installed package size
installed size is 7.1Mb
sub-directories of 1Mb or more:
extdata 2.8Mb
libs 2.8Mb
installed package size
installed size is 7.1Mb
sub-directories of 1Mb or more:
extdata 2.8Mb
libs 2.8Mb
installed package size
installed size is 5.5Mb
sub-directories of 1Mb or more:
extdata 2.8Mb
libs 1.2Mb
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Check History
WARNING 8 OK · 3 NOTE · 3 WARNING · 0 ERROR · 0 FAILURE Mar 9, 2026
Rd cross-references
Missing link(s) in Rd file 'LocusInfo.Rd':
‘[GenomicFeatures]{makeTxDbFromGFF}’
See section 'Cross-references' in the 'Writing R Extensions' manual.
Rd cross-references
Undeclared packages ‘polymapR’, ‘BSgenome’ in Rd xrefs
Missing link(s) in Rd file 'LocusInfo.Rd':
‘[GenomicFeatures]{makeTxDbFromGFF}’
See section 'Cross-references' in the 'Writing R Extensions' manual.
Rd cross-references
Missing link(s) in Rd file 'LocusInfo.Rd':
‘[GenomicFeatures]{makeTxDbFromGFF}’
See section 'Cross-references' in the 'Writing R Extensions' manual.
installed package size
installed size is 7.1Mb
sub-directories of 1Mb or more:
extdata 2.8Mb
libs 2.8Mb
installed package size
installed size is 7.1Mb
sub-directories of 1Mb or more:
extdata 2.8Mb
libs 2.8Mb
installed package size
installed size is 5.5Mb
sub-directories of 1Mb or more:
extdata 2.8Mb
libs 1.2Mb