#' Sample NxtSE object using the example reference and example bam files
#'
#' This function reproduces the data stored in the inst/extdata directory.
#' This data includes:
#'
#' * COV files produced by processing the example BAM dataset
#' * The NxtSE object produced by analysing the BAM dataset using the SpliceWiz
#' workflow
#'
#' Note the Non-PolyA reference files (contained within
#' "inst/extra-input-files") are from
#' [IRFinder](https://github.com/williamritchie/IRFinder)
#' @examples
#' se <- readRDS(
#' system.file("extdata", "example_NxtSE.Rds", package = "SpliceWiz")
#' )
#' se2 <- SpliceWiz_example_NxtSE()
#' identical(se, se2) # should return TRUE
#' @seealso
#' [makeSE] for an outline of how to reproduce this data using the SpliceWiz
#' workflow
make_example_NxtSE <- function() {
require(SpliceWiz)
bams <- SpliceWiz_example_bams()
buildRef(
fasta = chrZ_genome(), gtf = chrZ_gtf(),
reference_path = file.path(tempdir(), "Reference")
)
processBAM(
bams$path, bams$sample,
reference_path = file.path(tempdir(), "Reference"),
output_path = file.path(tempdir(), "SpliceWiz_Output"),
overwrite = TRUE, n_threads = 1
)
expr <- findSpliceWizOutput(file.path(tempdir(), "SpliceWiz_Output"))
collateData(
expr,
reference_path = file.path(tempdir(), "Reference"),
output_path = file.path(tempdir(), "Collated_output")
)
se <- makeSE(collate_path = file.path(tempdir(), "Collated_output"))
# Save COV files
file.copy(
expr$cov_file,
file.path("../extdata", basename(expr$cov_file)),
overwrite = TRUE
)
# De-identify COV files for validity once tempdir() no longer exists:
covfile(se) <- rep("", 6)
# Convert from HDF5-linked se to in-memory se:
se <- realize_NxtSE(se, includeJunctions = TRUE)
saveRDS(se, "../extdata/example_NxtSE.Rds")
# Make example NxtSE with novel splice detection
collateData(
expr,
reference_path = file.path(tempdir(), "Reference"),
output_path = file.path(tempdir(), "Collated_output_novel"),
novelSplicing = TRUE
)
se <- makeSE(collate_path = file.path(tempdir(), "Collated_output_novel"))
# De-identify COV files for validity:
covfile(se) <- rep("", 6)
# Convert from HDF5-linked se to in-memory se:
se <- realize_NxtSE(se, includeJunctions = TRUE)
saveRDS(se, "../extdata/example_NxtSE_novel.Rds")
}
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