tests/testthat/test-map_df_to_list.R

In qtl2convert: Convert Data among QTL Mapping Packages

context("Convert map data frame to list")

test_that("map_df_to_list works", {

    df <-  structure(list(marker = c("JAX00240989", "JAX00240649", "UNCJPD009180",
                          "JAX00240804", "JAX00240610", "UNCHS003854", "UNCHS003852", "UNCHS003846",
                          "JAX00482049", "JAX00482064", "JAX00281864", "ICR260", "JAX00014570",
                          "JAX00281798", "ICR4249", "JAX00708681", "JAX00708630r", "UNCHS048201",
                          "JAX00176676", "UNCHS048205"), chr = c("1", "1", "1", "1", "1",
                                                         "2", "2", "2", "2", "2", "10", "10", "10",
                                                         "10", "10", "X", "X", "X", "X", "X"),
                          Mb_GRC38 = c(5.379217, 3.454984, 5.754074, 4.334891,
                          3.266608, 4.118437, 4.115724, 3.74537, 3.23375, 3.362696, 4.306508,
                          3.5931, 3.993759, 4.631578, 4.666669, 6.845222, 6.369421, 6.536718,
                          6.05422, 6.586892),
                          cM = c(0.424118388815167, 0.041241020125091,
                          0.466051450603133, 0.0654810203913158, 0.0241660935186957, 0.182846980321827,
                          0.182407517001796, 0.130917988391064, 0.000412833594312019, 0.000640569383198255,
                          0.0163163877989646, 0.00740695778637858, 0.0124106069176088,
                          0.0203760400795549, 0.0208142757155046, 0.827432787823843, 0.235740657791282,
                          0.397500188730613, 0.0507409752570731, 0.501406880974154)),
                     .Names = c("marker", "chr", "Mb_GRC38", "cM"), class = "data.frame",
                     row.names = c(NA, -20L))


    expected <- structure(list(`1` = structure(c(0.424118388815167, 0.041241020125091,
                               0.466051450603133, 0.0654810203913158, 0.0241660935186957),
                               .Names = c("JAX00240989", "JAX00240649", "UNCJPD009180", "JAX00240804", "JAX00240610")),
                               `2` = structure(c(0.182846980321827, 0.182407517001796, 0.130917988391064,
                               0.000412833594312019, 0.000640569383198255),
                               .Names = c("UNCHS003854", "UNCHS003852", "UNCHS003846", "JAX00482049", "JAX00482064")),
                               `10` = structure(c(0.0163163877989646, 0.00740695778637858,
                               0.0124106069176088, 0.0203760400795549, 0.0208142757155046),
                               .Names = c("JAX00281864", "ICR260", "JAX00014570", "JAX00281798",
                               "ICR4249")),
                               X = structure(c(0.827432787823843, 0.235740657791282,
                               0.397500188730613, 0.0507409752570731, 0.501406880974154),
                               .Names = c("JAX00708681",
                               "JAX00708630r", "UNCHS048201", "JAX00176676", "UNCHS048205"
                               ))), .Names = c("1", "2", "10", "X"))
    attr(expected, "is_x_chr") <- c("1"=FALSE, "2"=FALSE, "10"=FALSE, "X"=TRUE)

    expect_equal(map_df_to_list(df), expected)


    # same thing with character string positions in the input
    df <-  structure(list(marker = c("JAX00240989", "JAX00240649", "UNCJPD009180",
                          "JAX00240804", "JAX00240610", "UNCHS003854", "UNCHS003852", "UNCHS003846",
                          "JAX00482049", "JAX00482064", "JAX00281864", "ICR260", "JAX00014570",
                          "JAX00281798", "ICR4249", "JAX00708681", "JAX00708630r", "UNCHS048201",
                          "JAX00176676", "UNCHS048205"), chr = c("1", "1", "1", "1", "1",
                                                         "2", "2", "2", "2", "2", "10", "10", "10",
                                                         "10", "10", "X", "X", "X", "X", "X"),
                          Mb_GRC38 = c("5.379217", "3.454984", "5.754074", "4.334891",
                          "3.266608", "4.118437", "4.115724", "3.74537", "3.23375", "3.362696", "4.306508",
                          "3.5931", "3.993759", "4.631578", "4.666669", "6.845222", "6.369421", "6.536718",
                          "6.05422", "6.586892"),
                          cM = c("0.424118388815167", "0.041241020125091",
                          "0.466051450603133", "0.0654810203913158", "0.0241660935186957", "0.182846980321827",
                          "0.182407517001796", "0.130917988391064", "0.000412833594312019", "0.000640569383198255",
                          "0.0163163877989646", "0.00740695778637858", "0.0124106069176088",
                          "0.0203760400795549", "0.0208142757155046", "0.827432787823843", "0.235740657791282",
                          "0.397500188730613", "0.0507409752570731", "0.501406880974154")),
                     .Names = c("marker", "chr", "Mb_GRC38", "cM"), class = "data.frame",
                     row.names = c(NA, -20L))

    expect_equal(map_df_to_list(df), expected)

    # give error if position column not found
    expect_error(map_df_to_list(df, pos_column="pos"))


    # same thing with marker names as row names
    rownames(df) <- df$marker
    df <- df[,c("chr", "Mb_GRC38", "cM")]
    expect_equal(map_df_to_list(df, marker_column=NULL), expected)

    # give error if marker column not found
    expect_error(map_df_to_list(df))

})