create_config {FLAMES} | R Documentation |
Create Configuration File From Arguments
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 )
outdir |
the destination directory for the configuratio nfile |
do_genome_align |
Boolean. Specifies whether to run the genome alignment step. |
do_isoform_id |
Boolean. Specifies whether to run the isoform identification step. |
do_read_realign |
Boolean. Specifies whether to run the read realignment step. |
do_transcript_quanti |
Boolean. Specifies whether to run the transcript quantification step. |
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 |
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
.
file path to the config file created
# 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)