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)Value
A SummarizedExperiment object, a SingleCellExperiment object,
or a list of SingleCellExperiment objects.
Examples
pipeline <- example_pipeline(type = "BulkPipeline")
#> Writing configuration parameters to: /tmp/RtmpgpEV0i/file25bf6888c57f/config_file_9663.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
#> Creating junction bed file from GFF3 annotation.
#> Aligning sample sample1 -> /tmp/RtmpgpEV0i/file25bf6888c57f/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/RtmpgpEV0i/file25bf6888c57f/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/RtmpgpEV0i/file25bf6888c57f/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
#> 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
#> Realigning sample sample1 -> /tmp/RtmpgpEV0i/file25bf6888c57f/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/RtmpgpEV0i/file25bf6888c57f/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/RtmpgpEV0i/file25bf6888c57f/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
se <- experiment(pipeline)