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GregFaGregFa
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Merge pull request #45 from GregFa/main
Updated test
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‎src/BigRiverQTL.jl

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using BulkLMM
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using DataFrames, JSON, CSV
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using Statistics
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using Distributed
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using LinearAlgebra
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import StatsBase: sample
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‎src/plots/plots_eqtl.jl

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- `threshold` is the LOD threshold value, default is `5.0``.
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"""
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function plot_eQTL(multiLODs::Array{Float64, 2}, dfpInfo::DataFrame, dfgInfo::DataFrame;
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function plot_eQTL(multiLODs::Array{Float64, 2}, dfpInfo::Pmap, dfgInfo::Gmap;
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kwargs...)
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return plot_eQTL(multiLODs,pmap2df(dfpInfo), gmap2df(dfgInfo); kwargs...)

‎test/data/BXD/ReadMe.md

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## BXD mouse recombinant inbred lines
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Genotype and phenotype data for the mouse BXD recombinant inbred
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lines, from [GeneNetwork](http://gn2.genenetwork.org).
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### File format
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See the [R/qtl2 input file format](https://kbroman.org/qtl2/assets/vignettes/input_files.html).
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### Citation
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Need to add a citation.
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### Use with [R/qtl2](https://kbroman.org/qtl2)
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Load these data into R directly from the web as follows:
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```r
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library(qtl2)
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file <- paste0("https://raw.githubusercontent.com/rqtl/",
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"qtl2data/main/BXD/bxd.zip")
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bxd <- read_cross2(file)
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```

‎test/data/BXD/bxd.json

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{
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"description": "BXD mouse data from GeneNetwork",
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"crosstype": "risib",
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"sep": ",",
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"na.strings": ["-", "NA"],
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"comment.char": "#",
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"geno": "bxd_geno.csv",
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"gmap": "bxd_gmap.csv",
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"pmap": "bxd_pmap.csv",
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"pheno": "bxd_pheno.csv",
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"phenocovar": "bxd_phenocovar.csv",
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"alleles": ["B", "D"],
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"x_chr": "X",
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"genotypes": {
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"B": 1,
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"D": 2
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},
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"geno_transposed": true,
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"cross_info": {
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"file": "bxd_crossinfo.csv",
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"BxD": 0
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}
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}

‎test/data/BXD/bxd_crossinfo.csv

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# Cross info for BXD data
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#(all lines formed from cross between female B and male D)
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# nrow 198
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# ncol 2
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id,cross_direction
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BXD1,BxD
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BXD2,BxD
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BXD5,BxD
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BXD6,BxD
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BXD8,BxD
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BXD9,BxD
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BXD11,BxD
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BXD12,BxD
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BXD13,BxD
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BXD14,BxD
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BXD15,BxD
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BXD16,BxD
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BXD18,BxD
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BXD19,BxD
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BXD20,BxD
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BXD21,BxD
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BXD22,BxD
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BXD23,BxD
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BXD24,BxD
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BXD24a,BxD
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BXD25,BxD
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BXD27,BxD
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BXD28,BxD
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BXD29,BxD
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BXD30,BxD
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BXD31,BxD
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BXD32,BxD
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BXD33,BxD
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BXD34,BxD
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BXD35,BxD
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BXD36,BxD
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BXD37,BxD
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BXD38,BxD
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BXD39,BxD
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BXD40,BxD
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BXD41,BxD
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BXD42,BxD
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BXD43,BxD
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BXD44,BxD
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BXD45,BxD
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BXD48,BxD
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BXD48a,BxD
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BXD49,BxD
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BXD50,BxD
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BXD51,BxD
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BXD52,BxD
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BXD53,BxD
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BXD54,BxD
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BXD55,BxD
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BXD56,BxD
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BXD59,BxD
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BXD60,BxD
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BXD61,BxD
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BXD62,BxD
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BXD63,BxD
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BXD64,BxD
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BXD65,BxD
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BXD65a,BxD
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BXD65b,BxD
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BXD73a,BxD
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BXD128a,BxD
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BXD176,BxD
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BXD177,BxD
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BXD180,BxD
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BXD183,BxD
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BXD201,BxD
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BXD216,BxD
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BXD217,BxD
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BXD218,BxD
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BXD219,BxD
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BXD220,BxD

‎test/data/BXD/bxd_geno.csv

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