tests/testthat/test-reduce_markers.R

In rqtl/qtl2geno: Treatment of Marker Genotypes for QTL Experiments

context("reduce markers")

test_that("reduce_markers works", {

    map <- list(c1=c(marker=5),
                c2=c(marker1=5, marker2=7))
    wts <- list(1, c(1,2))
    expect_equal(reduce_markers(map), map)
    expect_equal(reduce_markers(map, wts, 3),
                 list(c1=c(marker=5), c2=c(marker2=7)))

    grav2 <- read_cross2(system.file("extdata", "grav2.zip", package="qtl2geno"))

    RNGkind("Mersenne-Twister")
    set.seed(20151205)
    # use proportion typed as weights, but randomize a bit so there are no ties
    prtyped <- lapply(grav2$geno, function(a) colMeans(!is.na(a) & a>0) + runif(ncol(a), 0, 0.1))

    # expected results at min_dist=0.5
    expected <- structure(list(`1` = structure(c(0, 6.250674, 9.303868, 12.577629,
                               18.39283, 19.648542, 25.23229, 25.882095, 35.669554, 36.631747,
                               44.511901, 50.602339, 53.631519, 57.405778, 62.323561, 67.24062,
                               72.296762, 76.255226, 81.273196, 81.900811, 88.639045, 90.914789,
                               97.121385, 99.711975, 104.80612, 109.519692),
                               .Names = c("PVV4","AXR-1", "HH.335C-Col/PhyA", "EC.480C", "EC.66C", "GD.86L", "CH.160L-Col",
                               "CC.98L-Col/101C", "AD.121C", "AD.106L-Col", "GB.112L", "GD.97L",
                               "EG.113L/115C", "CD.89C", "BF.206L-Col", "CH.200C", "EC.88C",
                               "GD.160C", "HH.375L", "CH.215L", "BF.116C", "GH.157L-Col", "CC.318C",
                               "CD.173L/175C-Col", "GH.127L-Col/ADH", "HH.360L-Col")),
                               `2` = structure(c(0, 6.241796, 11.678237, 12.929907, 13.543347, 14.160672, 14.77799,
                               16.350906, 17.282463, 19.850147, 23.453866, 25.685578, 27.258244,
                               30.511191, 31.128921, 35.085099, 37.651404, 39.551472, 41.451601,
                               42.701885, 47.01718, 47.638238, 49.221621, 52.14781, 55.429739,
                               62.530948),
                               .Names = c("AD.156C", "BF.325L", "GH.580L", "DF.225L",
                               "BH.145C", "FD.306L", "BH.460L", "FD.81L", "BF.105C", "CH.284C",
                               "FD.222L-Col", "EG.66L", "CH.65C", "CH.1500C", "BF.221L", "FD.85C",
                               "GB.150L-Col", "FD.150C", "GD.460L-Col", "CH.145L-Col/150C",
                               "BH.195L-Col", "GD.298C", "GH.247L", "BH.120L-Col", "DF.140C",
                               "EC.235L-Col/247C")),
                               `3` = structure(c(0, 2.613844, 7.343692,
                               8.291564, 11.480925, 15.051063, 16.346984, 18.094189, 18.776988,
                               21.422012, 22.0854, 25.665317, 28.194604, 30.995068, 34.670912,
                               38.086009, 39.704548, 43.418084, 44.350416, 45.574261, 48.653207,
                               49.640633, 50.30031, 52.688082, 55.438502, 58.346108, 59.596912,
                               66.588704, 68.795163, 70.695509, 71.31314, 72.897197, 75.144036,
                               76.392762),
                               .Names = c("DF.77C", "GB.120C-Col", "EG.75L", "CH.322C",
                               "FD.111L-Col/136C", "CC.266L", "BF.270L-Col/271C", "CC.110L/127C",
                               "EC.58C", "GH.321L/323C-Col", "GH.226C/227L-Col", "EC.83C/84L",
                               "GD.318C/320L", "AD.92L", "BF.148C", "CD.800C", "BF.134C-Col",
                               "EG.122C", "GD.113C-Col", "FD.97C-Col", "DF.250L", "DF.76L",
                               "BF.128C", "HH.102C", "GD.296C-Col", "GH.172C", "FD.98C", "AD.182C",
                               "GH.58C-Col", "HH.171C-Col/173L", "AD.495L-Col", "AD.112L-Col",
                               "BH.109L-Col", "HH.90L-Col")),
                               `4` = structure(c(0, 6.388021,
                               17.889888, 18.507213, 22.755474, 27.797576, 30.442727, 34.758259,
                               35.375581, 39.942822, 40.635774, 45.254346, 46.537827, 48.152558,
                               53.206339, 56.459811, 60.771852, 67.771693, 73.668364),
                               .Names = c("ANL2",
                               "GH.250C", "HH.161L", "CC.388L", "EC.306L", "BH.92L-Col", "FD.154L",
                               "CH.238C", "GH.263C-Col", "SC5", "DF.108L-Col", "AD.307C", "AD.115L-Col",
                               "FD.167L-Col", "CH.70L/71C-Col", "GH.433L-Col", "GB.490C", "GB.750C",
                               "BH.342C/347L-Col")),
                               `5` = structure(c(0, 2.94061, 5.263751,
                               6.232987, 11.517411, 12.450901, 13.120403, 17.456274, 18.082939,
                               21.390456, 23.32081, 28.452586, 33.209409, 34.154297, 38.533295,
                               41.782964, 45.506147, 51.937046, 53.180697, 56.869545, 57.82089,
                               59.761176, 61.70335, 63.311005, 65.25314, 69.302896, 70.2914,
                               76.061598, 76.680571, 77.933341, 78.55132, 79.168573, 80.418873,
                               81.991829, 82.92342, 85.155018, 87.390432, 93.991816, 95.563679,
                               101.176465, 102.460924, 103.094847, 103.932196, 107.488998),
                               .Names = c("FD.207L",
                               "CH.690C", "AD.292L", "BH.144L", "EC.198L-Col", "BH.180C", "BH.325L",
                               "BH.107L-Col", "BF.269C", "AD.114C-Col", "CC.400L-Col", "EG.117L",
                               "GH.473C", "GH.117C", "GH.121L-Col", "DF.154C", "HH.480C", "BH.96L-Col",
                               "CC.188L", "EG.410C", "DF.300C", "GB.59C", "CD.179L", "EC.96L",
                               "CC.216C", "CC.277L-Col", "DFR", "AD.254C", "AD.75C-Col", "GD.350L-Col",
                               "CC.540C-Col", "GB.223C", "DF.450C", "HH.445L-Col", "GD.118C",
                               "CC.262C", "GB.102L-Col/105C", "HH.143C", "BF.168L-Col", "DF.119L",
                               "CH.331L-Col", "GD.222C-Col", "g2368", "HH.122C/120L"))),
                          .Names = c("1","2", "3", "4", "5"))

    attr(expected, "is_x_chr") <- attr(grav2$gmap, "is_x_chr")

    expect_equal( reduce_markers(grav2$gmap, prtyped, 0.5), expected)

})