Nothing
context("summary.fst_genoprob")
test_that("summary.fst_genoprob works", {
library(qtl2)
# load data and create pseudomarker map
iron <- read_cross2(system.file("extdata", "iron.zip", package="qtl2"))
gmap_w_pmar <- insert_pseudomarkers(iron$gmap, step=1)
# create directory to hold results
fst_dir <- file.path(tempdir(), "iron_genoprob")
while(dir.exists(fst_dir)) {
fst_dir <- paste0(fst_dir, sample(LETTERS, 1))
}
dir.create(fst_dir)
probs_fst <- calc_genoprob_fst(iron, "iron", fst_dir, gmap_w_pmar, error_prob=0.002,
overwrite=TRUE)
aprobs_fst <- genoprob_to_alleleprob_fst(probs_fst, "iron_aprob", fst_dir, overwrite=TRUE)
path_probs <- file.path(fst_dir, "iron")
path_aprobs <- file.path(fst_dir, "iron_aprob")
expect_equal(summary(probs_fst),
structure(list(path = path_probs, crosstype = "f2",
chr = c("1", "2", "3", "4", "5", "6", "7", "8", "9", "10",
"11", "12", "13", "14", "15", "16", "17", "18", "19", "X"),
n_ind = 284L,
n_gen = c(`1` = 3L, `2` = 3L, `3` = 3L, `4` = 3L, `5` = 3L,
`6` = 3L, `7` = 3L, `8` = 3L, `9` = 3L, `10` = 3L,
`11` = 3L, `12` = 3L, `13` = 3L, `14` = 3L, `15` = 3L,
`16` = 3L, `17` = 3L, `18` = 3L, `19` = 3L, X = 6L),
n_mar = c(`1` = 86L, `2` = 39L, `3` = 31L, `4` = 44L, `5` = 46L,
`6` = 27L, `7` = 58L, `8` = 83L, `9` = 58L, `10` = 35L,
`11` = 63L, `12` = 40L, `13` = 24L, `14` = 34L, `15` = 34L,
`16` = 48L, `17` = 37L, `18` = 28L, `19` = 36L, X = 30L),
alleleprobs = FALSE), class = c("summary.fst_genoprob", "list"))
)
expect_equal(summary(aprobs_fst),
structure(list(path = path_aprobs, crosstype = "f2",
chr = c("1", "2", "3", "4", "5", "6", "7", "8", "9", "10",
"11", "12", "13", "14", "15", "16", "17", "18", "19", "X"),
n_ind = 284L,
n_gen = c(`1` = 2L, `2` = 2L, `3` = 2L, `4` = 2L, `5` = 2L,
`6` = 2L, `7` = 2L, `8` = 2L, `9` = 2L, `10` = 2L,
`11` = 2L, `12` = 2L, `13` = 2L, `14` = 2L, `15` = 2L,
`16` = 2L, `17` = 2L, `18` = 2L, `19` = 2L, X = 2L),
n_mar = c(`1` = 86L, `2` = 39L, `3` = 31L, `4` = 44L, `5` = 46L,
`6` = 27L, `7` = 58L, `8` = 83L, `9` = 58L, `10` = 35L,
`11` = 63L, `12` = 40L, `13` = 24L, `14` = 34L, `15` = 34L,
`16` = 48L, `17` = 37L, `18` = 28L, `19` = 36L, X = 30L),
alleleprobs = TRUE), class = c("summary.fst_genoprob", "list"))
)
# clean up
unlink(fst_dir, recursive=TRUE)
})
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.