Nothing
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))
})
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