Create SummarizedExperiment object from FLAMES output folder

Create SummarizedExperiment object from FLAMES output folder

Usage

create_se_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 SummarizedExperiment object

Examples

# download the two fastq files, move them to a folder to be merged together
temp_path <- tempfile()
bfc <- BiocFileCache::BiocFileCache(temp_path, ask = FALSE)
file_url <-
  "https://raw.githubusercontent.com/OliverVoogd/FLAMESData/master/data"
# download the required fastq files, and move them to new folder
fastq1 <- bfc[[names(BiocFileCache::bfcadd(bfc, "Fastq1", paste(file_url, "fastq/sample1.fastq.gz", sep = "/")))]]
fastq2 <- bfc[[names(BiocFileCache::bfcadd(bfc, "Fastq2", paste(file_url, "fastq/sample2.fastq.gz", sep = "/")))]]
annotation <- bfc[[names(BiocFileCache::bfcadd(bfc, "annot.gtf", paste(file_url, "SIRV_isoforms_multi-fasta-annotation_C_170612a.gtf", sep = "/")))]]
genome_fa <- bfc[[names(BiocFileCache::bfcadd(bfc, "genome.fa", paste(file_url, "SIRV_isoforms_multi-fasta_170612a.fasta", sep = "/")))]]
fastq_dir <- paste(temp_path, "fastq_dir", sep = "/") # the downloaded fastq files need to be in a directory to be merged together
dir.create(fastq_dir)
file.copy(c(fastq1, fastq2), fastq_dir)
#> [1] TRUE TRUE
unlink(c(fastq1, fastq2)) # the original files can be deleted

outdir <- tempfile()
dir.create(outdir)
if (!any(is.na(sys_which(c("minimap2", "k8"))))) {
  se <- bulk_long_pipeline(
    annotation = annotation, fastq = fastq_dir, outdir = outdir, genome_fa = genome_fa,
    config_file = system.file("extdata/SIRV_config_default.json", package = "FLAMES")
  )

  se_2 <- create_se_from_dir(outdir = outdir, annotation = annotation)
}