Get pipeline results — experiment • FLAMES

This function returns the results of the pipeline as a SummarizedExperiment object, a SingleCellExperiment object, or a list of SingleCellExperiment objects, depending on the pipeline type.

Usage

experiment(pipeline)

# S4 method for class 'FLAMES.Pipeline'
experiment(pipeline)

# S4 method for class 'FLAMES.MultiSampleSCPipeline'
experiment(pipeline)

Arguments

pipeline: A FLAMES.Pipeline object.

Value

A SummarizedExperiment object, a SingleCellExperiment object, or a list of SingleCellExperiment objects.

Examples

pipeline <- example_pipeline(type = "BulkPipeline")
#> Writing configuration parameters to:  /tmp/RtmpA5lNG6/file329025b294fb/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
pipeline <- run_FLAMES(pipeline)
#> ── Running step: genome_alignment @ Mon Jun 23 02:41:42 2025 ───────────────────
#> Creating junction bed file from GFF3 annotation.
#> Aligning sample sample1 -> /tmp/RtmpA5lNG6/file329025b294fb/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/file329025b294fb/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/file329025b294fb/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 02:41:42 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 02:41:43 2025 ───────────────────
#> Realigning sample sample1 -> /tmp/RtmpA5lNG6/file329025b294fb/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/file329025b294fb/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/file329025b294fb/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 02:41:43 2025 ──────────
se <- experiment(pipeline)