# test script for combineContigs.R - testcases are NOT comprehensive!
test_that("combineTCR works", {
data("contig_list")
trial1 <- combineTCR(
input.data = lapply(contig_list[1:3], head),
samples = c("P17B", "P17L", "P18B")
)
expected1 <- getdata("combineContigs", "combineTCR_list_expected")
expect_identical(trial1, expected1)
trial2 <- combineTCR(
head(contig_list[[1]]), samples = "P17B"
)[[1]]
expected2 <- expected1[[1]]
expect_identical(trial2, expected2)
trial3 <- combineTCR(
input.data = lapply(contig_list[1:3], head),
samples = c("P17B", "P17L", "P18B"),
filterMulti = TRUE
)
expect_identical(trial3, getdata("combineContigs", "combineTCR_list_filterMulti"))
trial4 <- combineTCR(
input.data = lapply(contig_list[1:3], head),
samples = c("P17B", "P17L", "P18B"),
removeNA = TRUE
)
expect_identical(trial4, getdata("combineContigs", "combineTCR_list_removeNA"))
trial5 <- combineTCR(
input.data = contig_list[1:2],
samples = c("P17B", "P17L"),
filterNonproductive = FALSE
)
expect_identical(trial5, getdata("combineContigs", "combineTCR_list_nonproductive"))
})
# TODO combineTCR & combineBCR (need more edge cases, different args, errors, etc.)
# TODO combineTCR for non-10x formats
test_that("combineBCR works", {
BCR <- read.csv("https://www.borch.dev/uploads/contigs/b_contigs.csv")
bcr.trial1 <- combineBCR(BCR,
samples = "Patient1")
bcr.trial1[[1]] <- bcr.trial1[[1]][order(bcr.trial1[[1]]$barcode),]
expect_identical(bcr.trial1, getdata("combineContigs", "combineBCR_list_expected"))
})
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