Create SummarizedExperiment
object from FLAMES
output folder
Source: R/methods-SingleCellPipeline.R
create_se_from_dir.Rd
Create SummarizedExperiment
object from FLAMES
output folder
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.
Examples
ppl <- example_pipeline("BulkPipeline")
#> Writing configuration parameters to: /tmp/RtmpyvgB0f/file76e3553cecd1/config_file_30435.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 Aug 25 09:35:02 2025 ───────────────────
#> Creating junction bed file from GFF3 annotation.
#> Aligning sample sample1 -> /tmp/RtmpyvgB0f/file76e3553cecd1/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/RtmpyvgB0f/file76e3553cecd1/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/RtmpyvgB0f/file76e3553cecd1/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 Aug 25 09:35:02 2025 ─────────────
#> ── Running step: read_realignment @ Mon Aug 25 09:35:02 2025 ───────────────────
#> Realigning sample sample1 -> /tmp/RtmpyvgB0f/file76e3553cecd1/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/RtmpyvgB0f/file76e3553cecd1/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/RtmpyvgB0f/file76e3553cecd1/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 Aug 25 09:35:03 2025 ──────────
se1 <- experiment(ppl)
se2 <- create_se_from_dir(ppl@outdir, ppl@annotation)