Selecting one chromosome | Subsetting by ind, chr, mar | Binding by columns or rows | Looking under the hood | Paths | Direct construction of the fst database | Genome scans
Package: qtl2fst 0.31-1
Karl W Broman
qtl2fst: Database Storage of Genotype Probabilities for QTL Mapping
Uses the 'fst' package to store genotype probabilities on disk for the 'qtl2' package. These genotype probabilities are a central data object for mapping quantitative trait loci (QTL), but they can be quite large. The facilities in this package enable the genotype probabilities to be stored on disk, leading to reduced memory usage with only a modest increase in computation time.
Authors:
qtl2fst_0.31-1.tar.gz
qtl2fst_0.31-1.zip(r-4.7)qtl2fst_0.31-1.zip(r-4.6)qtl2fst_0.31-1.zip(r-4.5)
qtl2fst_0.31-1.tgz(r-4.6-any)qtl2fst_0.31-1.tgz(r-4.5-any)
qtl2fst_0.31-1.tar.gz(r-4.7-any)qtl2fst_0.31-1.tar.gz(r-4.6-any)
qtl2fst_0.31-1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
qtl2fst/json (API)
| # Install 'qtl2fst' in R: |
| install.packages('qtl2fst', repos = c('https://rqtl.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/rqtl/qtl2fst/issues
Last updated from:56b7332ab5. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 168 | ||
| source / vignettes | OK | 201 | ||
| linux-release-x86_64 | OK | 196 | ||
| macos-release-arm64 | OK | 110 | ||
| macos-oldrel-arm64 | OK | 106 | ||
| windows-devel | OK | 110 | ||
| windows-release | OK | 101 | ||
| windows-oldrel | OK | 102 | ||
| wasm-release | OK | 102 |
Exports:calc_genoprob_fstcbind.fst_genoprobfst_extractfst_filesfst_genoprobfst_genoprob_restorefst_pathfst_restorefst2calc_genoprobgenoprob_to_alleleprob_fstrbind.fst_genoprobreplace_pathsubset_fst_genoprob
Dependencies:bitbit64blobcachemclicpp11data.tableDBIfastmapfstfstcoregluejsonlitelifecyclememoisepkgconfigqtl2RcppRcppEigenrlangRSQLitevctrsyaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Calculate conditional genotype probabilities and write to fst database | calc_genoprob_fst |
| Join genotype probabilities for different chromosomes | cbind.fst_genoprob |
| Extract genotype probabilities from fst database | fst2calc_genoprob fst_extract |
| List files used in fst_genoprob object | fst_files |
| Store genotype probabilities in fst database | fst_genoprob |
| Path used in fst_genoprob object | fst_path |
| Restore fst_genoprob object to original dimensions. | fst_genoprob_restore fst_restore |
| Convert genotype probabilities to allele probabilities and write to fst database | genoprob_to_alleleprob_fst |
| Join genotype probabilities for different individuals | rbind.fst_genoprob |
| Replace the path used in fst_genoprob object | replace_path |
| Subsetting genotype probabilities | subset.fst_genoprob subset_fst_genoprob |
| Summary of an fst_genoprob object | summary.fst_genoprob |
