Create Configuration File From Arguments

Usage

create_config(outdir, type = "sc_3end", ...)

Arguments

outdir

the destination directory for the configuratio nfile

type

use an example config, available values:

"sc_3end": - config for 10x 3' end ONT reads
"SIRV": - config for the SIRV example reads

...

Configuration parameters.

seed: - Integer. Seed for minimap2.
threads: - Number of threads to use.
do_barcode_demultiplex: - Boolean. Specifies whether to run the barcode demultiplexing step.
do_genome_alignment: - Boolean. Specifies whether to run the genome alignment step. TRUE is recommended
do_gene_quantification: - Boolean. Specifies whether to run gene quantification using the genome alignment results. TRUE is recommended
do_isoform_identification: - Boolean. Specifies whether to run the isoform identification step. TRUE is recommended
bambu_isoform_identification: - Boolean. Whether to use Bambu for isoform identification.
multithread_isoform_identification: - Boolean. Whether to use FLAMES' new multithreaded Cpp implementation for isoform identification.
do_read_realignment: - Boolean. Specifies whether to run the read realignment step. TRUE is recommended
do_transcript_quantification: - Boolean. Specifies whether to run the transcript quantification step. TRUE is recommended
barcode_parameters: - List. Parameters for barcode demultiplexing passed to find_barcode (except fastq, barcodes_file, stats_out, reads_out) and threads, which are set by the pipeline, see ?find_barcode for more details.
generate_raw_isoform: - Boolean. Whether to generate all isoforms for debugging purpose.
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: - 0, 1 or -1. 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

Value

file path to the config file created

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. Default values from extdata/config_sclr_nanopore_3end.json will be used for unprovided parameters.

Examples

# create the default configuration file
outdir <- tempdir()
config <- create_config(outdir)
#> Writing configuration parameters to:  /tmp/RtmpoS7Kzz/config_file_8045.json