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
## Not run: 
config <- create_config(
    getwd(), 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 0.99.31 Index]