create_config {FLAMES} | R Documentation

## Create Configuration File From Arguments

### Description

Create Configuration File From Arguments

### Usage

    create_config(
      outdir,
      do_genome_align,
      do_isoform_id,
      do_read_realign,
      do_transcript_quanti,
      gen_raw_isoform,
      has_UMI,
      MAX_DIST,
      MAX_TS_DIST,
      MAX_SPLICE_MATCH_DIST,
      min_fl_exon_len,
      Max_site_per_splice,
      Min_sup_cnt,
      Min_cnt_pct,
      Min_sup_pct,
      strand_specific,
      remove_incomp_reads,
      use_junctions,
      no_flank,
      use_annotation,
      min_tr_coverage,
      min_read_coverage
    )

### Arguments

`outdir` | the destination directory for the configuratio nfile
`do_genome_align` | Boolean. Specifies whether to run the genome alignment step. `TRUE` is recommended
`do_isoform_id` | Boolean. Specifies whether to run the isoform identification step. `TRUE` is recommended
`do_read_realign` | Boolean. Specifies whether to run the read realignment step. `TRUE` is recommended
`do_transcript_quanti` | Boolean. Specifies whether to run the transcript quantification step. `TRUE` is recommended
`gen_raw_isoform` | Boolean.
`has_UMI` | Boolean. Specifies if the data contains UMI.
`MAX_DIST` | Maximum distance allowed when merging splicing sites in isoform consensus clustering.
`MAX_TS_DIST` | Maximum distance allowed when merging transcript start/end position in isoform consensus clustering.
`MAX_SPLICE_MATCH_DIST` | Maximum distance allowed when merging splice site called from the data and the reference annotation.
`min_fl_exon_len` | Minimum length for the first exon outside the gene body in reference annotation. This is to correct the alignment artifact
`Max_site_per_splice` | Maximum transcript start/end site combinations allowed per splice chain
`Min_sup_cnt` | Minimum number of read support an isoform decrease this number will significantly increase the number of isoform detected.
`Min_cnt_pct` | Minimum percentage of count for an isoform relative to total count for the same gene.
`Min_sup_pct` | Minimum percentage of count for an splice chain that support a given transcript start/end site combination.
`strand_specific` | 1, -1 or 0. 1 indicates if reads are in the same strand as mRNA, -1 indicates reads are reverse complemented, 0 indicates reads are not strand specific.
`remove_incomp_reads` | The strenge of truncated isoform filtering. larger number means more stringent filtering.
`use_junctions` | whether to use known splice junctions to help correct the alignment results
`no_flank` | Boolean. for synthetic spike-in data. refer to Minimap2 document for detail
`use_annotation` | Boolean. whether to use reference to help annotate known isoforms
`min_tr_coverage` | Minimum percentage of isoform coverage for a read to be aligned to that isoform
`min_read_coverage` | Minimum percentage of read coverage for a read to be uniquely aligned to that isoform

### Details

Create a list object containing the arguments supplied in a format usable for the FLAMES pipeline. Also writes the object to a JSON file, which is located with the prefix 'config_' in the supplied `outdir`.

### Value

file path to the config file created

### Examples

    # create the default configuartion file
    output = tempfile()
    ## Not run:
    config <- create_config(
        tempfile(), TRUE, TRUE,
        TRUE, TRUE,
        TRUE, FALSE,
        10, 100, 10,
        40, 3, 10,
        0.01, 0.2, 1, 5,
        TRUE, TRUE,
        TRUE, 0.75, 0.75
    )

    ## End(Not run)

[Package FLAMES version 1.0.2 Index]