Nothing
context("Calculate genotype frequencies")
test_that("calc_geno_freq works for an intercross", {
iron <- read_cross2(system.file("extdata", "iron.zip", package="qtl2"))
pr <- calc_genoprob(iron, err=0.002)
# omit_x works?
expect_equal(calc_geno_freq(pr[,1:19]), calc_geno_freq(pr, omit_x=TRUE))
expect_equal(calc_geno_freq(pr[,1:19], "marker"), calc_geno_freq(pr, "marker", omit_x=TRUE))
# by individual
expected <- structure(list(A = structure(c(0.265431865621607, 0.179999497125949,
0.437768300719857, 0.530653642640462,
0.296799833658536, 0.289346860233589),
.Dim = 2:3, .Dimnames = list(c("88", "105"), c("SS", "SB", "BB"))),
X = structure(c(0, 0, 0, 0, 0, 0, 0, 0, 0.5, 0.5, 0.5, 0.5),
.Dim = c(2L, 6L), .Dimnames = list(c("88", "105"),
c("SS", "SB", "BS", "BB",
"SY", "BY")))),
.Names = c("A", "X"))
expect_equal(calc_geno_freq(pr[c(88,105),]), expected$A)
expect_equal(calc_geno_freq(pr[c(88,105),], omit_x=TRUE), expected$A)
expect_equal(calc_geno_freq(pr[c(88,105),], omit_x=FALSE), expected)
# by marker
expected <- structure(list(A = structure(c(0.268363278479528, 0.278689258334566,
0.48461632550778, 0.477608930381241,
0.247020396012691, 0.243701811284194),
.Dim = 2:3, .Dimnames = list(c("D19Mit68", "D19Mit37"),
c("SS", "SB", "BB"))),
X = structure(c(0.121465495590373, 0.117994689355019,
0.139097884691317, 0.142568690926671,
0.112701216600633, 0.116172022835987,
0.116172022835987, 0.112701216600633,
0.239547079613345, 0.253430304554763,
0.271016300668345, 0.257133075726927),
.Dim = c(2L, 6L), .Dimnames = list(c("DXMit16", "DXMit186"),
c("SS", "SB", "BS", "BB",
"SY", "BY")))),
.Names = c("A", "X"))
expect_equal(calc_geno_freq(pr[,c(19,"X")], "marker"), expected$A)
expect_equal(calc_geno_freq(pr[,c(19,"X")], "marker", omit_x=TRUE), expected$A)
expect_equal(calc_geno_freq(pr[,c(19,"X")], "marker", omit_x=FALSE), expected)
# genotype probs -> allele probs
apr <- genoprob_to_alleleprob(pr)
# allele frequencies by individual
expected <- structure(c(0.484316015981535, 0.44532631844618, 0.515683984018465, 0.55467368155382),
.Dim = c(2L, 2L), .Dimnames = list(c("88", "105"), c("S", "B")))
expect_equal(calc_geno_freq(apr[c(88,105),]), expected)
# include X chr
expected <- structure(c(0.484791288224519, 0.446983096675083, 0.515208711775481,0.553016903324917),
.Dim = c(2L, 2L), .Dimnames = list(c("88","105"), c("S", "B")))
expect_equal(calc_geno_freq(apr[c(88,105),], omit_x=FALSE), expected)
# allele frequencies by marker
expected <- structure(c(0.510671441233419, 0.517493723525186, 0.489328558766582, 0.482506276474814),
.Dim = c(2L, 2L), .Dimnames = list(c("D19Mit68", "D19Mit37"), c("S", "B")))
expect_equal(calc_geno_freq(apr[,c(19,"X")], "marker"), expected)
# include X chr
expected <- structure(c(0.510671441233419, 0.517493723525186, 0.486912125849693, 0.500795350791111,
0.489328558766582, 0.482506276474814, 0.513087874150307, 0.499204649208889),
.Dim = c(4L, 2L), .Dimnames = list(c("D19Mit68", "D19Mit37", "DXMit16", "DXMit186"),
c("S", "B")))
expect_equal(calc_geno_freq(apr[,c(19,"X")], "marker", omit_x=FALSE), expected)
})
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