inst/scripts/doqtl2.md

In byandell/qtl2shiny: Shiny interface for 'qtl2' Fine Mapping

title: "R/doqtl2 migration" author: "Brian S Yandell, http://www.stat.wisc.edu/~yandell" date: "January 2017" output: html_document

migrated to R/qtl2pattern

file | function ----------------- | -------- shinyGeneExon.R | plot_gene_exon shinyGeneRegion.R | get_mgi_features shinyPattern.R | scan_pattern shinyProbs.R | get_snpprobs read_probs read_probs36 shinySNPAllele.R | get_gene_exon_snp get_top_snps_tbl snpprob_collapse shinyScan1Plot.R | listof_scan1coefCC shinySetup.R | get_pheno shinyTopFeature.R | merge_feature

function | file | use ----------------- | -------- | -------- get_gene_exon_snp | gene_exon.R | call get_mgi_features get_mgi_features | get_mgi_features.R | extract from SQLite get_pheno | get_traits.R | get selected phenotypes get_snpprobs | snpinfo.R | snpprobs for SNPs, InDels, SVs get_top_snps_tbl | top_snps_tbl.R | get top SNP info based on LMMs listof_scan1coefCC | listof_scan1coefCC.R | create list of scan1coefCC objects merge_feature | merge_feature.R | merge SNP LOD and other information plot_gene_exon | gene_exon.R | plot genes and exons read_probs | read_probs.R | read genoprob object for RDS read_probs36 | read_probs.R | read genoprob object for RDS scan_pattern | scan_pattern.R | genome scan by pattern set snpprob_collapse | genoprob_to_patternprob.R | collapse from alleles to SNPs

Want scan_pattern to look like plot_snpasso with pattern="all".

Need to work on geno and exon stuff to meld with plot_genes.

byandell/qtl2shiny documentation built on June 11, 2025, 4:54 a.m.