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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| r-devel-macos-arm64 | OK |
| r-devel-windows-x86_64 | OK |
| r-oldrel-macos-arm64 | NOTE |
| r-oldrel-macos-x86_64 | NOTE |
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| r-patched-linux-x86_64 | OK |
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Check details (5 non-OK)
installed package size
installed size is 7.5Mb
sub-directories of 1Mb or more:
extdata 2.8Mb
libs 3.2Mb
Rd cross-references
Package unavailable to check Rd xrefs: ‘txdbmaker’
installed package size
installed size is 7.2Mb
sub-directories of 1Mb or more:
extdata 2.8Mb
libs 2.9Mb
package dependencies
Package suggested but not available for checking: ‘txdbmaker’
installed package size
installed size is 5.5Mb
sub-directories of 1Mb or more:
extdata 2.8Mb
libs 1.2Mb
Check History
NOTE 11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 24, 2026
installed package size
installed size is 7.5Mb
sub-directories of 1Mb or more:
extdata 2.8Mb
libs 3.2Mb
package dependencies
Package suggested but not available for checking: ‘txdbmaker’
installed package size
installed size is 5.5Mb
sub-directories of 1Mb or more:
extdata 2.8Mb
libs 1.2Mb
WARNING 8 OK · 3 NOTE · 3 WARNING · 0 ERROR · 0 FAILURE Mar 10, 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