Package: qtl2pattern 1.2.2
Brian S Yandell
qtl2pattern: Pattern Support for 'qtl2' Package
Routines in 'qtl2' to study allele patterns in quantitative trait loci (QTL) mapping over a chromosome. Useful in crosses with more than two alleles to identify how sets of alleles, genetically different strands at the same locus, have different response levels. Plots show profiles over a chromosome. Can handle multiple traits together. See <https://github.com/byandell/qtl2pattern>.
Authors:
qtl2pattern_1.2.2.tar.gz
qtl2pattern_1.2.2.zip(r-4.5)qtl2pattern_1.2.2.zip(r-4.4)qtl2pattern_1.2.2.zip(r-4.3)
qtl2pattern_1.2.2.tgz(r-4.4-any)qtl2pattern_1.2.2.tgz(r-4.3-any)
qtl2pattern_1.2.2.tar.gz(r-4.5-noble)qtl2pattern_1.2.2.tar.gz(r-4.4-noble)
qtl2pattern_1.2.2.tgz(r-4.4-emscripten)qtl2pattern_1.2.2.tgz(r-4.3-emscripten)
qtl2pattern.pdf |qtl2pattern.html✨
qtl2pattern/json (API)
| # Install 'qtl2pattern' in R: |
| install.packages('qtl2pattern', repos = c('https://byandell-sysgen.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/byandell/qtl2pattern/issues
Last updated 1 years agofrom:44e129ddc5. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 11 2024 |
| R-4.5-win | OK | Nov 11 2024 |
| R-4.5-linux | OK | Nov 11 2024 |
| R-4.4-win | OK | Nov 11 2024 |
| R-4.4-mac | OK | Nov 11 2024 |
| R-4.3-win | OK | Nov 11 2024 |
| R-4.3-mac | OK | Nov 11 2024 |
Exports:allele1autoplot.feature_tblautoplot.gene_exonautoplot.merge_featureautoplot.scan1patterncreate_probs_query_funcgene_exongenoprob_to_patternprobggplot_allele1ggplot_feature_tblggplot_gene_exonggplot_merge_featureggplot_scan1patternmerge_featurepattern_labelpattern_sdpread_fastscan1patternsdp_to_logicalsdp_to_patternsnpprob_collapsetop_snps_pattern
Dependencies:assertthatbitbit64blobcachemclicolorspacecpp11data.tableDBIdplyrfansifarverfastmapfstfstcoregenericsggplot2gluegtableisobandjsonlitelabelinglatticelifecyclemagrittrMASSMatrixmemoisemgcvmunsellnlmepillarpkgconfigplogrpurrrqtl2qtl2fstR6RColorBrewerRcppRcppEigenrlangRSQLitescalesstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Allele plot for SNPs, alleles and allele pairs | allele1 autoplot.allele1 ggplot_allele1 |
| Create a function to query genotype probabilities | create_probs_query_func |
| Get exons for set of genes | autoplot.gene_exon gene_exon ggplot_gene_exon subset.gene_exon summary.gene_exon |
| Collapse genoprob according to pattern | genoprob_to_patternprob |
| Match features with SNPs | get_feature_snp |
| Match genes with SNPs | get_gene_snp |
| Helper function to set gene locations on plot. | get.gene.locations |
| Plot of merge_feature object | autoplot.merge_feature ggplot_merge_feature merge_feature summary.merge_feature |
| Plot scan pattern usign ggplot2 | autoplot.scan1pattern ggplot_scan1pattern scan1pattern summary.scan1pattern |
| Extract pattern of diplotypes | pattern_diplos pattern_haplos |
| Turn genotype probabilities into labels | pattern_label pattern_sdp |
| Read fast database with possible rownames | read_fast |
| Read genotype probability object from file | read_probs |
| Convert sdp to pattern | sdp_to_logical sdp_to_pattern |
| Convert SNP info to map | snpinfo_to_map |
| Collapse genoprob according to pattern | snpprob_collapse |
| Summary of features with SNP information | summary.feature_snp |
| Summary of features | autoplot.feature_tbl ggplot_feature_tbl subset.feature_tbl summary.feature_tbl |
| Summary of genes overlapping SNPs | summary.gene_snp |
| Top SNPs organized by allele pattern | subset.top_snps_pattern summary.top_snps_pattern top_snps_pattern |