Create SummarizedExperiment object from FLAMES output folder

Create SummarizedExperiment object from FLAMES output folder

Usage

create_se_from_dir(outdir, annotation, quantification = "FLAMES")

Arguments

outdir: The folder containing FLAMES output files
annotation: (Optional) the annotation file that was used to produce the output files
quantification: (Optional) the quantification method used to generate the output files (either "FLAMES" or "Oarfish".). If not specified, the function will attempt to determine the quantification method.

Value

a SummarizedExperiment object

Examples

ppl <- example_pipeline("BulkPipeline")
#> Writing configuration parameters to:  /tmp/RtmpA5lNG6/file329023d99379/config_file_12944.json 
#> Configured steps: 
#> 	genome_alignment: TRUE
#> 	isoform_identification: TRUE
#> 	read_realignment: TRUE
#> 	transcript_quantification: TRUE
#> samtools not found, will use Rsamtools package instead
ppl <- run_FLAMES(ppl)
#> ── Running step: genome_alignment @ Mon Jun 23 02:41:39 2025 ───────────────────
#> Creating junction bed file from GFF3 annotation.
#> Aligning sample sample1 -> /tmp/RtmpA5lNG6/file329023d99379/sample1_align2genome.bam
#> Warning: samtools not found, using Rsamtools instead, this could be slower and might fail for large BAM files.
#> Sorting BAM files by genome coordinates with 1 threads...
#> Indexing bam files
#> Aligning sample sample2 -> /tmp/RtmpA5lNG6/file329023d99379/sample2_align2genome.bam
#> Warning: samtools not found, using Rsamtools instead, this could be slower and might fail for large BAM files.
#> Sorting BAM files by genome coordinates with 1 threads...
#> Indexing bam files
#> Aligning sample sample3 -> /tmp/RtmpA5lNG6/file329023d99379/sample3_align2genome.bam
#> Warning: samtools not found, using Rsamtools instead, this could be slower and might fail for large BAM files.
#> Sorting BAM files by genome coordinates with 1 threads...
#> Indexing bam files
#> ── Running step: isoform_identification @ Mon Jun 23 02:41:39 2025 ─────────────
#> Import genomic features from the file as a GRanges object ... 
#> OK
#> Prepare the 'metadata' data frame ... 
#> OK
#> Make the TxDb object ... 
#> Warning: genome version information is not available for this TxDb object
#> OK
#> ── Running step: read_realignment @ Mon Jun 23 02:41:40 2025 ───────────────────
#> Realigning sample sample1 -> /tmp/RtmpA5lNG6/file329023d99379/sample1_realign2transcript.bam
#> Warning: samtools not found, using Rsamtools instead, this could be slower and might fail for large BAM files.
#> Skipped sorting BAM files.
#> Realigning sample sample2 -> /tmp/RtmpA5lNG6/file329023d99379/sample2_realign2transcript.bam
#> Warning: samtools not found, using Rsamtools instead, this could be slower and might fail for large BAM files.
#> Skipped sorting BAM files.
#> Realigning sample sample3 -> /tmp/RtmpA5lNG6/file329023d99379/sample3_realign2transcript.bam
#> Warning: samtools not found, using Rsamtools instead, this could be slower and might fail for large BAM files.
#> Skipped sorting BAM files.
#> ── Running step: transcript_quantification @ Mon Jun 23 02:41:40 2025 ──────────
se1 <- experiment(ppl)
se2 <- create_se_from_dir(ppl@outdir, ppl@annotation)