consolidate_lymphgen.RdReplace the lymphgen column in the incoming metadata with classification for additional samples.
consolidate_lymphgen(sample_table, derived_data_path = "", verbose = TRUE)Input data frame with metadata.
Optional argument specifying the path to a folder with files following the pattern *lymphgen.txt.
Default is TRUE.
A data frame with a supplemented lymphGen column.
Supplement the "lymphgen" column of the metadata with classification for additional samples. Expects at least to have columns "patient_id" to bind on, and "lymphgen" to supplement the data on.
metadata = get_gambl_metadata()
consolidate_lymphgen(sample_table = metadata)
#> No external data path was provided, using default path /projects/nhl_meta_analysis_scratch/gambl/results_local/icgc_dart/derived_and_curated_metadata/
#> Found these file(s) with lymphgen information: METADATA_3_cohorts_lymphgen.txt
#> # A tibble: 1,671 × 110
#> compression bam_available patient_id sample_id seq_type capture_space
#> <chr> <lgl> <chr> <chr> <chr> <chr>
#> 1 bam TRUE 00-14595 00-14595_tumorA genome none
#> 2 cram TRUE 00-14595 00-14595_tumorB genome none
#> 3 cram TRUE 00-14595 00-14595_tumorC genome none
#> 4 bam TRUE 00-14595 00-14595_tumorD genome none
#> 5 cram TRUE 00-15201 00-15201_tumorA genome none
#> 6 cram TRUE 00-15201 00-15201_tumorB genome none
#> 7 bam TRUE 00-16220 00-16220_tumorB genome none
#> 8 cram TRUE 00-20702 00-20702T genome none
#> 9 cram TRUE 00-23442 00-23442_tumorA genome none
#> 10 cram TRUE 00-23442 00-23442_tumorB genome none
#> # ℹ 1,661 more rows
#> # ℹ 104 more variables: genome_build <chr>, tissue_status <chr>, cohort <chr>,
#> # library_id <chr>, pathology <chr>, time_point <chr>, protocol <chr>,
#> # ffpe_or_frozen <chr>, read_length <dbl>, strandedness <chr>,
#> # seq_source_type <chr>, EBV_status_inf <chr>, link_name <chr>,
#> # data_path <chr>, unix_group <chr>, biopsy_id <chr>, fastq_link_name <chr>,
#> # fastq_data_path <chr>, COO_consensus <chr>, DHITsig_consensus <chr>, …