Tests every path a cohort references: the file-like columns of its sample
map (fastq_1, bam, and similar), and every entry of cohort@paths.
Never errors; a summary is reported when something is missing.
Arguments
- cohort
A Cohort object.
- cols
Optional character vector of
sample_mapcolumn names to check as paths, overriding the default set of recognized path columns (fastq_1,fastq_2,bam,cram,vcf,matrix_dir,h5).
Value
A tibble with one row per checked path and columns source
("sample_map" or "paths"), key (sample_id, or the name in
cohort@paths), column (the sample_map column, NA for a
cohort@paths entry), path, and exists. exists is NA for a
missing (NA) path, so an unset path is not read as a broken one.
Examples
data(example_cohort)
check_paths(example_cohort)
#> 24 paths not found. See the exists column.
#> # A tibble: 24 × 5
#> source key column path exists
#> <chr> <chr> <chr> <chr> <lgl>
#> 1 sample_map WES_R001_T fastq_1 wes_r001_t_R1.fastq.gz FALSE
#> 2 sample_map WES_R001_N fastq_1 wes_r001_n_R1.fastq.gz FALSE
#> 3 sample_map SNRNA_R001 fastq_1 snrna_r001_R1.fastq.gz FALSE
#> 4 sample_map WES_R002_T fastq_1 wes_r002_t_R1.fastq.gz FALSE
#> 5 sample_map WES_R002_N fastq_1 wes_r002_n_R1.fastq.gz FALSE
#> 6 sample_map SNRNA_R002 fastq_1 snrna_r002_R1.fastq.gz FALSE
#> 7 sample_map WES_M001_T fastq_1 wes_m001_t_R1.fastq.gz FALSE
#> 8 sample_map WES_M001_N fastq_1 wes_m001_n_R1.fastq.gz FALSE
#> 9 sample_map SNRNA_M001 fastq_1 snrna_m001_R1.fastq.gz FALSE
#> 10 sample_map WES_M002_T fastq_1 wes_m002_t_R1.fastq.gz FALSE
#> # ℹ 14 more rows