Config YAML file parsing.
Public fields
tool(
character(1))
Tool name.config(
list())
Config list.raw_schemas_all(
tibble())
All raw schemas for tool.tidy_schemas_all(
tibble())
All tidy schemas for tool.
Methods
Examples
tool <- "isofox"
conf <- Config$new(tool)
conf$get_raw_patterns()
#> # A tibble: 8 × 2
#> name value
#> <chr> <chr>
#> 1 summary "\\.isf\\.summary\\.csv$"
#> 2 genedata "\\.isf\\.gene_data\\.csv$"
#> 3 transdata "\\.isf\\.transcript_data\\.csv$"
#> 4 altsj "\\.isf\\.alt_splice_junc\\.csv$"
#> 5 retintron "\\.isf\\.retained_intron\\.csv$"
#> 6 fusionsall "\\.isf\\.fusions\\.csv$"
#> 7 fusionspass "\\.isf\\.pass_fusions\\.csv$"
#> 8 genecollection "\\.isf\\.gene_collection\\.csv$"
conf$get_raw_versions()
#> # A tibble: 8 × 2
#> name value
#> <chr> <chr>
#> 1 summary latest
#> 2 genedata latest
#> 3 transdata latest
#> 4 altsj latest
#> 5 retintron latest
#> 6 fusionsall latest
#> 7 fusionspass latest
#> 8 genecollection latest
conf$get_raw_descriptions()
#> # A tibble: 8 × 2
#> name value
#> <chr> <chr>
#> 1 summary QC summary.
#> 2 genedata Gene level data.
#> 3 transdata Transcript level data.
#> 4 altsj Alternate splice junctions.
#> 5 retintron Retained introns.
#> 6 fusionsall All fusions.
#> 7 fusionspass Passed fusions.
#> 8 genecollection Gene collection.
conf$get_raw_schemas_all()
#> # A tibble: 8 × 3
#> name version schema
#> <chr> <chr> <list>
#> 1 summary latest <tibble [16 × 2]>
#> 2 genedata latest <tibble [13 × 2]>
#> 3 transdata latest <tibble [18 × 2]>
#> 4 altsj latest <tibble [18 × 2]>
#> 5 retintron latest <tibble [10 × 2]>
#> 6 fusionsall latest <tibble [31 × 2]>
#> 7 fusionspass latest <tibble [29 × 2]>
#> 8 genecollection latest <tibble [15 × 2]>
conf$get_raw_schema("summary")
#> # A tibble: 16 × 2
#> field type
#> <chr> <chr>
#> 1 SampleId c
#> 2 QcStatus c
#> 3 TotalFragments d
#> 4 DuplicateFragments d
#> 5 SplicedFragmentPerc d
#> 6 UnsplicedFragmentPerc d
#> 7 AltFragmentPerc d
#> 8 ChimericFragmentPerc d
#> 9 SplicedGeneCount d
#> 10 ReadLength d
#> 11 FragLength5th d
#> 12 FragLength50th d
#> 13 FragLength95th d
#> 14 EnrichedGenePercent d
#> 15 MedianGCRatio d
#> 16 ForwardStrandPercent d
conf$are_raw_schemas_valid()
#> [1] TRUE
conf$get_tidy_descriptions()
#> # A tibble: 8 × 2
#> name value
#> <chr> <chr>
#> 1 summary QC summary.
#> 2 genedata Gene level data.
#> 3 transdata Transcript level data.
#> 4 altsj Alternate splice junctions.
#> 5 retintron Retained introns.
#> 6 fusionsall All fusions.
#> 7 fusionspass Passed fusions.
#> 8 genecollection Gene collection.
conf$get_tidy_schemas_all()
#> # A tibble: 8 × 4
#> name version tbl schema
#> <chr> <chr> <chr> <list>
#> 1 summary latest tbl1 <tibble [16 × 3]>
#> 2 genedata latest tbl1 <tibble [13 × 3]>
#> 3 transdata latest tbl1 <tibble [18 × 3]>
#> 4 altsj latest tbl1 <tibble [18 × 3]>
#> 5 retintron latest tbl1 <tibble [10 × 3]>
#> 6 fusionsall latest tbl1 <tibble [31 × 3]>
#> 7 fusionspass latest tbl1 <tibble [29 × 3]>
#> 8 genecollection latest tbl1 <tibble [15 × 3]>
conf$get_tidy_schema("summary")
#> # A tibble: 16 × 3
#> field type description
#> <chr> <chr> <chr>
#> 1 sample_id c "sample ID"
#> 2 qc_status c "QC status"
#> 3 frag_tot d "total fragments"
#> 4 frag_dup d "duplicate marked fragments"
#> 5 frag_spliced_pct d "fragment % supporting 1 or more known transcripts"
#> 6 frag_unspliced_pct d "fragment % not containing a splice junction and no…
#> 7 frag_alt_pct d "fragment % supporting an alternate splice junction…
#> 8 frag_chimeric_pct d "fragment % supporting a chimeric junction"
#> 9 spliced_gene_count d "count of spliced genes"
#> 10 read_length d "raw read length of fragments"
#> 11 frag_length_5th d "5th percentile of genic intronic fragment lengths"
#> 12 frag_length_50th d "50th percentile of genic intronic fragment lengths"
#> 13 frag_length_95th d "95th percentile of genic intronic fragment lengths"
#> 14 enriched_gene_pct d "fragment % supporting one of the following 6 genes…
#> 15 median_gc_ratio d "median GC ratio excluding the 6 highly enriched ge…
#> 16 forward_strand_pct d ""