Nothing
context("I/O of yaml/json control files")
test_that("write_control_file gives correct output for riself", {
dir <- tempdir()
file <- file.path(dir, "grav2.yaml")
on.exit(unlink(file))
# write file
write_control_file(file,
crosstype="riself",
geno_file="grav2_geno.csv",
gmap_file="grav2_gmap.csv",
pheno_file="grav2_pheno.csv",
phenocovar_file="grav2_phenocovar.csv",
geno_codes=c(L=1L, C=2L),
alleles=c("L", "C"),
na.strings=c("-", "NA"))
# read it back in
control <- read_control_file(file)
expected <- structure(list(crosstype = "riself", geno = "grav2_geno.csv",
pheno = "grav2_pheno.csv", phenocovar = "grav2_phenocovar.csv",
gmap = "grav2_gmap.csv", alleles = c("L", "C"),
genotypes = structure(list(L = 1L, C = 2L), .Names = c("L", "C")),
sep=",", na.strings = c("-", "NA"), comment.char="#"),
.Names = c("crosstype", "geno", "pheno", "phenocovar",
"gmap", "alleles", "genotypes", "sep", "na.strings", "comment.char"))
expect_equal(sort(names(control)), sort(names(expected)))
expected <- expected[names(control)]
expect_equal(control, expected)
})
test_that("write_control_file in JSON for riself", {
dir <- tempdir()
file <- file.path(dir, "grav2.json")
on.exit(unlink(file))
# write file
write_control_file(file,
crosstype="riself",
geno_file="grav2_geno.csv",
gmap_file="grav2_gmap.csv",
pheno_file="grav2_pheno.csv",
phenocovar_file="grav2_phenocovar.csv",
geno_codes=c(L=1L, C=2L),
alleles=c("L", "C"),
na.strings=c("-", "NA"))
# read it back in
control <- read_control_file(file)
expected <- structure(list(crosstype = "riself", geno = "grav2_geno.csv",
pheno = "grav2_pheno.csv", phenocovar = "grav2_phenocovar.csv",
gmap = "grav2_gmap.csv", alleles = c("L", "C"),
genotypes = structure(list(L = 1L, C = 2L), .Names = c("L", "C")),
sep=",",
na.strings = c("-", "NA"), comment.char="#"),
.Names = c("crosstype", "geno", "pheno", "phenocovar",
"gmap", "alleles", "genotypes", "sep", "na.strings", "comment.char"))
expect_equal(sort(names(control)), sort(names(expected)))
expected <- expected[names(control)]
expect_equal(control, expected)
})
test_that("write_control_file gives correct output for intercross", {
dir <- tempdir()
file <- file.path(dir, "iron.yaml")
on.exit(unlink(file))
# write file
write_control_file(file,
crosstype="f2",
geno_file="iron_geno.csv",
gmap_file="iron_gmap.csv",
pheno_file="iron_pheno.csv",
covar_file="iron_covar.csv",
phenocovar_file="iron_phenocovar.csv",
geno_codes=c(SS=1L, SB=2L, BB=3L),
sex_covar="sex",
sex_codes=c(f="female", m="male"),
crossinfo_covar="cross_direction",
crossinfo_codes=c("(SxB)x(SxB)"=0L, "(BxS)x(BxS)"=1L),
xchr="X",
alleles=c("S", "B"),
na.strings=c("-", "NA"))
# read it back in
control <- read_control_file(file)
expected <- structure(list(crosstype = "f2", geno = "iron_geno.csv", pheno = "iron_pheno.csv",
phenocovar = "iron_phenocovar.csv", covar = "iron_covar.csv",
gmap = "iron_gmap.csv", alleles = c("S", "B"),
genotypes = structure(list(SS = 1L, SB = 2L, BB = 3L), .Names = c("SS", "SB", "BB")),
sex = structure(list(covar = "sex", f = "female", m = "male"),
.Names = c("covar", "f", "m")),
cross_info = structure(list(covar = "cross_direction", `(SxB)x(SxB)` = 0L, `(BxS)x(BxS)` = 1L),
.Names = c("covar", "(SxB)x(SxB)", "(BxS)x(BxS)")),
x_chr = "X", sep=",", na.strings = c("-", "NA"), comment.char="#"),
.Names = c("crosstype", "geno", "pheno", "phenocovar",
"covar", "gmap", "alleles", "genotypes", "sex", "cross_info",
"x_chr", "sep", "na.strings", "comment.char"))
expect_equal(sort(names(control)), sort(names(expected)))
expected <- expected[names(control)]
expect_equal(control, expected)
})
test_that("write_control_file in JSON intercross", {
dir <- tempdir()
file <- file.path(dir, "iron.json")
on.exit(unlink(file))
# write file
write_control_file(file,
crosstype="f2",
geno_file="iron_geno.csv",
gmap_file="iron_gmap.csv",
pheno_file="iron_pheno.csv",
covar_file="iron_covar.csv",
phenocovar_file="iron_phenocovar.csv",
geno_codes=c(SS=1L, SB=2L, BB=3L),
sex_covar="sex",
sex_codes=c(f="female", m="male"),
crossinfo_covar="cross_direction",
crossinfo_codes=c("(SxB)x(SxB)"=0L, "(BxS)x(BxS)"=1L),
xchr="X",
alleles=c("S", "B"),
na.strings=c("-", "NA"))
# read it back in
control <- read_control_file(file)
expected <- structure(list(crosstype = "f2", geno = "iron_geno.csv", pheno = "iron_pheno.csv",
phenocovar = "iron_phenocovar.csv", covar = "iron_covar.csv",
gmap = "iron_gmap.csv", alleles = c("S", "B"),
genotypes = structure(list(SS = 1L, SB = 2L, BB = 3L), .Names = c("SS", "SB", "BB")),
sex = structure(list(covar = "sex", f = "female", m = "male"),
.Names = c("covar", "f", "m")),
cross_info = structure(list(covar = "cross_direction", `(SxB)x(SxB)` = 0L, `(BxS)x(BxS)` = 1L),
.Names = c("covar", "(SxB)x(SxB)", "(BxS)x(BxS)")),
x_chr = "X", sep=",", na.strings = c("-", "NA"), comment.char="#"),
.Names = c("crosstype", "geno", "pheno", "phenocovar",
"covar", "gmap", "alleles", "genotypes", "sex", "cross_info",
"x_chr", "sep", "na.strings", "comment.char"))
expect_equal(sort(names(control)), sort(names(expected)))
expected <- expected[names(control)]
expect_equal(control, expected)
})
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