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Create SummarizedExperiment object from FLAMES output folder

Source: R/methods-SingleCellPipeline.R
create_se_from_dir.Rd

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/RtmpXoUSS6/file9b284af32e1d/config_file_39720.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 @ Fri Sep 12 07:59:06 2025 ───────────────────
#> Creating junction bed file from GFF3 annotation.
#> Aligning sample sample1 -> /tmp/RtmpXoUSS6/file9b284af32e1d/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/RtmpXoUSS6/file9b284af32e1d/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/RtmpXoUSS6/file9b284af32e1d/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 @ Fri Sep 12 07:59:06 2025 ─────────────
#> ── Running step: read_realignment @ Fri Sep 12 07:59:06 2025 ───────────────────
#> Realigning sample sample1 -> /tmp/RtmpXoUSS6/file9b284af32e1d/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/RtmpXoUSS6/file9b284af32e1d/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/RtmpXoUSS6/file9b284af32e1d/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 @ Fri Sep 12 07:59:07 2025 ──────────
se1 <- experiment(ppl)
se2 <- create_se_from_dir(ppl@outdir, ppl@annotation)