test_that("set returnFilterColumns works", {
orig <- returnFilterColumns(edb)
returnFilterColumns(edb) <- TRUE
expect_equal(TRUE, returnFilterColumns(edb))
returnFilterColumns(edb) <- FALSE
expect_equal(FALSE, returnFilterColumns(edb))
expect_error(returnFilterColumns(edb) <- "d")
expect_error(returnFilterColumns(edb) <- c(TRUE, FALSE))
## Restore the "original" setting
returnFilterColumns(edb) <- orig
})
test_that("returnFilterColumns works with_genes", {
orig <- returnFilterColumns(edb)
returnFilterColumns(edb) <- FALSE
## What happens if we use a GRangesFilter with return filter cols FALSE?
grf <- GRangesFilter(GRanges(17, IRanges(59106500, 59155300)),
type = "within")
res <- genes(edb, filter = grf)
expect_equal(res$gene_id,
c("ENSG00000224738", "ENSG00000182628", "ENSG00000252212",
"ENSG00000211514", "ENSG00000207996"))
cols <- c("gene_id", "gene_name")
res <- genes(edb, filter = grf, return.type = "data.frame",
columns = cols)
## Expect only the columns
expect_equal(colnames(res), cols)
returnFilterColumns(edb) <- TRUE
res <- genes(edb, filter = grf, return.type = "data.frame",
columns = cols)
## Now I expect also the gene coords.
expect_equal(colnames(res), c(cols, "gene_seq_start", "gene_seq_end",
"seq_name", "seq_strand"))
## Use a gene biotype filter
gbt <- GeneBiotypeFilter("protein_coding")
returnFilterColumns(edb) <- TRUE
res <- genes(edb, filter = list(gbt, grf), return.type = "data.frame",
columns = cols)
expect_equal(res$gene_name, "SKA2")
expect_equal(colnames(res), c(cols, "gene_biotype", "gene_seq_start",
"gene_seq_end", "seq_name", "seq_strand"))
returnFilterColumns(edb) <- FALSE
res <- genes(edb, filter = list(gbt, grf), return.type = "data.frame",
columns = cols)
expect_equal(colnames(res), cols)
returnFilterColumns(edb) <- orig
})
test_that("returnFilterColumns works with_tx", {
orig <- returnFilterColumns(edb)
returnFilterColumns(edb) <- FALSE
## What happens if we use a GRangesFilter with return filter cols FALSE?
## grf <- GRangesFilter(GRanges(17, IRanges(57180000, 57233000)),
## type = "within")
grf <- GRangesFilter(GRanges(17, IRanges(59106500, 59155300)),
type = "within")
res <- transcripts(edb, filter = grf)
cols <- c("tx_id", "gene_name")
res <- transcripts(edb, filter = grf, return.type = "data.frame",
columns = cols)
## Expect only the columns
expect_equal(colnames(res), cols)
returnFilterColumns(edb) <- TRUE
res <- transcripts(edb, filter = grf, return.type = "data.frame",
columns = cols)
## Now I expect also the gene coords.
expect_equal(colnames(res), c(cols, "tx_seq_start", "tx_seq_end", "seq_name",
"seq_strand"))
## Use a gene biotype filter
gbt <- GeneBiotypeFilter("protein_coding")
returnFilterColumns(edb) <- TRUE
res <- transcripts(edb, filter = list(gbt, grf), return.type = "data.frame",
columns = cols)
expect_equal(unique(res$gene_name), "SKA2")
expect_equal(colnames(res), c(cols, "gene_biotype", "tx_seq_start",
"tx_seq_end", "seq_name", "seq_strand"))
returnFilterColumns(edb) <- FALSE
res <- transcripts(edb, filter = list(gbt, grf), return.type = "data.frame",
columns = cols)
expect_equal(colnames(res), cols)
returnFilterColumns(edb) <- orig
})
test_that("returnFilterColumns works with exons", {
orig <- returnFilterColumns(edb)
returnFilterColumns(edb) <- FALSE
## What happens if we use a GRangesFilter with return filter cols FALSE?
## grf <- GRangesFilter(GRanges(17, IRanges(57180000, 57233000)),
## type = "within")
grf <- GRangesFilter(GRanges(17, IRanges(58982600, 59155300)),
type = "within")
res <- exons(edb, filter = grf)
cols <- c("exon_id", "gene_name")
res <- exons(edb, filter = grf, return.type = "data.frame",
columns = cols)
## Expect only the columns
expect_equal(colnames(res), cols)
returnFilterColumns(edb) <- TRUE
res <- exons(edb, filter = grf, return.type = "data.frame",
columns = cols)
## Now I expect also the gene coords.
expect_equal(colnames(res), c(cols, "exon_seq_start", "exon_seq_end",
"seq_name", "seq_strand"))
## Use a gene biotype filter
gbt <- GeneBiotypeFilter("protein_coding")
returnFilterColumns(edb) <- TRUE
res <- exons(edb, filter = list(gbt, grf), return.type = "data.frame",
columns = cols)
expect_equal(unique(res$gene_name), c("TRIM37", "SKA2"))
expect_equal(colnames(res), c(cols, "gene_biotype", "exon_seq_start",
"exon_seq_end", "seq_name", "seq_strand"))
returnFilterColumns(edb) <- FALSE
res <- exons(edb, filter = list(gbt, grf), return.type = "data.frame",
columns = cols)
expect_equal(colnames(res), cols)
returnFilterColumns(edb) <- orig
})
test_that("returnFilterColumns works with exonsBy", {
orig <- returnFilterColumns(edb)
returnFilterColumns(edb) <- FALSE
## What happens if we use a GRangesFilter with return filter cols FALSE?
grf <- GRangesFilter(GRanges(17, IRanges(58982600, 59155300)),
type = "within")
## By genes
cols <- c("exon_id", "gene_name")
res <- exonsBy(edb, by = "gene", filter = grf, columns = cols)
res <- unlist(res)
## Expect only the columns
expect_equal(colnames(mcols(res)), cols)
returnFilterColumns(edb) <- TRUE
res <- exonsBy(edb, by = "gene", filter = grf, columns = cols)
res <- unlist(res)
## Now I expect also the gene coords, but not the seq_name and seq_strand,
## as these are redundant with data which is in the GRanges!
expect_equal(colnames(mcols(res)), c(cols, "gene_seq_start", "gene_seq_end"))
## Use a gene biotype filter
gbt <- GeneBiotypeFilter("protein_coding")
returnFilterColumns(edb) <- TRUE
res <- unlist(exonsBy(edb, by = "gene", filter = list(gbt, grf), columns = cols))
expect_equal(unique(res$gene_name), c("TRIM37", "SKA2"))
expect_equal(colnames(mcols(res)), c(cols, "gene_biotype", "gene_seq_start",
"gene_seq_end"))
returnFilterColumns(edb) <- FALSE
res <- unlist(exonsBy(edb, by = "gene", filter = list(gbt, grf), columns = cols))
expect_equal(colnames(mcols(res)), cols)
## By tx
returnFilterColumns(edb) <- FALSE
cols <- c("exon_id", "gene_name")
res <- exonsBy(edb, by = "tx", filter = grf, columns = cols)
res <- unlist(res)
## Expect only the columns
expect_equal(colnames(mcols(res)), c(cols, "exon_rank"))
returnFilterColumns(edb) <- TRUE
res <- exonsBy(edb, by = "tx", filter = grf, columns = cols)
res <- unlist(res)
## Now I expect also the gene coords.
expect_equal(colnames(mcols(res)), c(cols, "tx_seq_start", "tx_seq_end",
"exon_rank"))
## Use a gene biotype filter
gbt <- GeneBiotypeFilter("protein_coding")
returnFilterColumns(edb) <- TRUE
res <- unlist(exonsBy(edb, by = "tx", filter = list(gbt, grf),
columns = cols))
expect_equal(unique(res$gene_name), c("TRIM37", "SKA2"))
expect_equal(colnames(mcols(res)), c(cols, "gene_biotype", "tx_seq_start",
"tx_seq_end", "exon_rank"))
returnFilterColumns(edb) <- FALSE
res <- unlist(exonsBy(edb, by = "tx", filter = list(gbt, grf),
columns = cols))
expect_equal(colnames(mcols(res)), c(cols, "exon_rank"))
returnFilterColumns(edb) <- orig
})
test_that("returnFilterColumns works with transcriptsBy", {
orig <- returnFilterColumns(edb)
returnFilterColumns(edb) <- FALSE
## What happens if we use a GRangesFilter with return filter cols FALSE?
## grf <- GRangesFilter(GRanges(17, IRanges(57180000, 57233000)),
## type = "within")
grf <- GRangesFilter(GRanges(17, IRanges(59106500, 59155300)),
type = "within")
## By genes
cols <- c("tx_id", "gene_name")
res <- transcriptsBy(edb, by = "gene", filter = grf, columns = cols)
res <- unlist(res)
## Expect only the columns
expect_equal(colnames(mcols(res)), cols)
returnFilterColumns(edb) <- TRUE
res <- transcriptsBy(edb, by = "gene", filter = grf, columns = cols)
res <- unlist(res)
## Now I expect also the gene coords.
expect_equal(colnames(mcols(res)), c(cols, "gene_seq_start", "gene_seq_end"))
## Use a gene biotype filter
gbt <- GeneBiotypeFilter("protein_coding")
returnFilterColumns(edb) <- TRUE
res <- unlist(transcriptsBy(edb, by = "gene", filter = list(gbt, grf),
columns = cols))
expect_equal(unique(res$gene_name), c("SKA2"))
expect_equal(colnames(mcols(res)),
c(cols, "gene_biotype", "gene_seq_start", "gene_seq_end"))
returnFilterColumns(edb) <- FALSE
res <- unlist(transcriptsBy(edb, by = "gene", filter = list(gbt, grf),
columns = cols))
expect_equal(colnames(mcols(res)), cols)
returnFilterColumns(edb) <- orig
})
test_that("returnFilterColumns works with_cdsBy", {
orig <- returnFilterColumns(edb)
## grf <- GRangesFilter(GRanges(17, IRanges(57180000, 57233000)),
## type = "within")
grf <- GRangesFilter(GRanges(17, IRanges(59106500, 59155300)),
type = "within")
## By tx
returnFilterColumns(edb) <- FALSE
cols <- c("gene_id", "gene_name")
res <- cdsBy(edb, by = "tx", filter = grf, columns = cols)
res <- unlist(res)
## Expect only the columns
expect_equal(colnames(mcols(res)), c(cols, "exon_id", "exon_rank"))
returnFilterColumns(edb) <- TRUE
res <- cdsBy(edb, by = "tx", filter = grf, columns = cols)
res <- unlist(res)
## Now I expect also the gene coords.
expect_equal(colnames(mcols(res)), c(cols, "tx_seq_start", "tx_seq_end",
"seq_name", "seq_strand", "exon_id",
"exon_rank"))
## Use a gene biotype filter
gbt <- GeneBiotypeFilter("protein_coding")
returnFilterColumns(edb) <- TRUE
res <- unlist(cdsBy(edb, by = "tx", filter = list(gbt, grf), columns = cols))
expect_equal(unique(res$gene_name), c("SKA2"))
expect_equal(colnames(mcols(res)), c(cols, "gene_biotype", "tx_seq_start",
"tx_seq_end", "seq_name", "seq_strand",
"exon_id", "exon_rank"))
returnFilterColumns(edb) <- FALSE
res <- unlist(cdsBy(edb, by = "tx", filter = list(gbt, grf), columns = cols))
expect_equal(colnames(mcols(res)), c(cols, "exon_id", "exon_rank"))
returnFilterColumns(edb) <- orig
})
test_that("returnFilterColumns works with threeUTRsByTranscript", {
orig <- returnFilterColumns(edb)
## grf <- GRangesFilter(GRanges(17, IRanges(57180000, 57233000)),
## type = "within")
grf <- GRangesFilter(GRanges(17, IRanges(59106500, 59155300)),
type = "within")
## By tx
returnFilterColumns(edb) <- FALSE
cols <- c("gene_id", "gene_name")
res <- threeUTRsByTranscript(edb, filter = grf, columns = cols)
res <- unlist(res)
## Expect only the columns
expect_equal(colnames(mcols(res)), c(cols, "exon_id", "exon_rank"))
returnFilterColumns(edb) <- TRUE
res <- threeUTRsByTranscript(edb, filter = grf, columns = cols)
res <- unlist(res)
## Now I expect also the gene coords.
expect_equal(colnames(mcols(res)), c(cols, "tx_seq_start", "tx_seq_end",
"seq_name", "seq_strand", "exon_id",
"exon_rank"))
## Use a gene biotype filter
gbt <- GeneBiotypeFilter("protein_coding")
returnFilterColumns(edb) <- TRUE
res <- unlist(threeUTRsByTranscript(edb, filter = list(gbt, grf),
columns = cols))
expect_equal(unique(res$gene_name), c("SKA2"))
expect_equal(colnames(mcols(res)), c(cols, "gene_biotype", "tx_seq_start",
"tx_seq_end", "seq_name", "seq_strand",
"exon_id", "exon_rank"))
returnFilterColumns(edb) <- FALSE
res <- unlist(threeUTRsByTranscript(edb, filter = list(gbt, grf),
columns = cols))
expect_equal(colnames(mcols(res)), c(cols, "exon_id", "exon_rank"))
returnFilterColumns(edb) <- orig
})
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