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Create SingleCellExperiment object from FLAMES output folder

Source: R/sc_long_pipeline.R
create_sce_from_dir.Rd

Create SingleCellExperiment object from FLAMES output folder

Usage

create_sce_from_dir(outdir, annotation)

Arguments

outdir

The folder containing FLAMES output files

annotation

(Optional) the annotation file that was used to produce the output files

Value

a list of SingleCellExperiment objects if multiple transcript matrices were found in the output folder, or a SingleCellExperiment object if only one were found

Examples

outdir <- tempfile()
dir.create(outdir)
bc_allow <- file.path(outdir, "bc_allow.tsv")
genome_fa <- file.path(outdir, "rps24.fa")
R.utils::gunzip(filename = system.file("extdata/bc_allow.tsv.gz", package = "FLAMES"), destname = bc_allow, remove = FALSE)
R.utils::gunzip(filename = system.file("extdata/rps24.fa.gz", package = "FLAMES"), destname = genome_fa, remove = FALSE)
annotation <- system.file("extdata/rps24.gtf.gz", package = "FLAMES")

if (!any(is.na(sys_which(c("minimap2", "k8"))))) {
    sce <- FLAMES::sc_long_pipeline(
        genome_fa = genome_fa,
        fastq = system.file("extdata/fastq", package = "FLAMES"),
        annotation = annotation,
        outdir = outdir,
        barcodes_file = bc_allow
    )
    sce_2 <- create_sce_from_dir(outdir, annotation)
}