Package: gbasics 1.2.1
Mark Bravington
gbasics: Genotype classes and support routines for CKMR
S3 classes for manipulating genetic data, primarily NGS SNPs (sequence counts and/or genotypes) but maybe more, plus support for other kin-finding/genotyping packages; ultimately meant for Close-Kin Mark-Recapture.
Authors:
gbasics_1.2.1.tar.gz
gbasics_1.2.1.zip(r-4.7)gbasics_1.2.1.zip(r-4.6)gbasics_1.2.1.zip(r-4.5)
gbasics_1.2.1.tgz(r-4.6-any)gbasics_1.2.1.tgz(r-4.5-any)
gbasics_1.2.1.tar.gz(r-4.7-any)gbasics_1.2.1.tar.gz(r-4.6-any)
gbasics_1.2.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
gbasics/json (API)
NEWS
| # Install 'gbasics' in R: |
| install.packages('gbasics', repos = c('https://markbravington.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/markbravington/gbasics/issues
- snpgarbage - Specimen 'snpgeno' object filled with garbage data
Last updated from:d381002207. Checks:7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | NOTE | 117 | ||
| source / vignettes | OK | 149 | ||
| linux-release-x86_64 | NOTE | 108 | ||
| macos-release-arm64 | NOTE | 80 | ||
| macos-oldrel-arm64 | NOTE | 77 | ||
| windows-devel | NOTE | 97 | ||
| windows-release | NOTE | 119 | ||
| windows-oldrel | NOTE | 74 | ||
| wasm-release | OK | 101 |
Exports:define_genotypesdiploidodiplosdiplos<-get_genotype_encodinginv_CDF_SPA2loc.armake_genopairerNGS_count_arNGS_count_ar.matrixprint.NGS_count_arread_snpgds2snpgenoread_vcf2NGS_count_arread_vcf2snpgenorenorm_SPArenorm_SPA_cumulridderrowid_fieldsnpgenosnpgeno.defaultstr.loc.arstr.NGS_count_arstr.snpgenounloc.arwith_rowid_field
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Genotype storage ultimately for Close-Kin Mark-Recapture | gbasics-package gbasics |
| Class for one diploid locus | diploido |
| Diploid genotype encodings | define_genotypes get_genotype_encoding |
| Create & manipulate locus-arrays | loc.ar unloc.ar |
| Mapping between pairs of possible genotypes and compressed form | make_genopairer |
| Next-Gen sequencer count data | NGS_count_ar NGS_count_ar.matrix print print.NGS_count_ar |
| Create a 'snpgeno' from 'snpgds' file or object | read_snpgds2snpgeno |
| Read VCF genotype data | read_vcf2NGS_count_ar read_vcf2snpgeno |
| Saddlepoint approximation support | inv_CDF_SPA2 renorm_SPA renorm_SPA_cumul |
| Parallel root-finder | ridder |
| Specimen 'snpgeno' object filled with garbage data | data snpgarbage |
| Class for SNP genotypes | diplos diplos<- set_rowid_field snpgeno snpgeno.default |
| Summaries for various genotype classes | str str.loc.ar str.NGS_count_ar str.snpgeno |
| Facilitate sample-based subscripting of sngpenos | rowid_field with_rowid_field |