Get GAMBL metadata. — og_get_gambl_metadata • GAMBLR.results

Return metadata for a selection of samples.

Usage

og_get_gambl_metadata(
  seq_type_filter = "genome",
  tissue_status_filter = "tumour",
  case_set,
  remove_benchmarking = TRUE,
  with_outcomes = TRUE,
  sample_flatfile,
  biopsy_flatfile,
  only_available = TRUE,
  seq_type_priority = "genome",
  from_flatfile
)

Arguments

seq_type_filter: Filtering criteria (default: all genomes).
tissue_status_filter: Filtering criteria for tissue status. Possible values are "tumour" (the default) or "normal".
case_set: Optional short name for a pre-defined set of cases avoiding any embargoed cases (current options: 'BLGSP-study', 'FL-study', 'DLBCL-study', 'FL-DLBCL-study', 'FL-DLBCL-all', 'DLBCL-unembargoed', 'BL-DLBCL-manuscript', 'MCL','MCL-CLL').
remove_benchmarking: By default the FFPE benchmarking duplicate samples will be dropped.
with_outcomes: Optionally join to gambl outcome data.
sample_flatfile: Optionally provide the full path to a sample table to use instead of the default.
biopsy_flatfile: Optionally provide the full path to a biopsy table to use instead of the default.
only_available: If TRUE, will remove samples with FALSE or NA in the bam_available column (default: TRUE).
seq_type_priority: For duplicate sample_id with different seq_type available, the metadata will prioritize this seq_type and drop the others. Possible values are "genome" or "capture".
from_flatfile: Deprecated (will be ignored)

Value

A data frame with metadata for each biopsy in GAMBL

compression: Format of the original data used as input for our analysis pipelines (cram, bam or fastq)
bam_available: Whether or not this file was available when last checked.
patient_id: The anonymized unique identifier for this patient. For BC samples, this will be Res ID.
sample_id: A unique identifier for the sample analyzed.
seq_type: The assay type used to produce this data (one of "genome","capture, "mrna", "promethION")
genome_build: The name of the genome reference the data were aligned to.
tissue_status: Whether the sample was atumour or normal.
cohort: Name for a group of samples that were added together (usually from a single study), often in the format pathology_cohort_descriptor.
library_id: The unique identifier for the sequencing library.
pathology: The diagnosis or pathology for the sample
time_point: Timing of biopsy in increasing alphabetical order (A = diagnosis, B = first relapse etc)
protocol: General protocol for library construction. e.g. "Ribodepletion", "PolyA", or "Genome"
ffpe_or_frozen: Whether the nucleic acids were extracted from a frozen or FFPE sample
read_length: The length of reads (required for RNA-seq libraries)
strandedness: Whether the RNA-seq librayr construction was strand-specific and, if so, which strand. Required for RNAseq; "positive", "negative", or "unstranded")
seq_source_type: Required for RNAseq. Usually the same value as ffpe_or_frozen but sometimes immunotube or sorted cells
data_path: Symbolic link to the bam or cram file (not usually relevant for GAMBLR)
link_name: Standardized naming for symbolic link (not usually relevant for GAMBLR)
data_path: Symbolic link to the fastq file (not usually relevant for GAMBLR)
fastq_link_name: Standardized naming for symbolic link for FASTQ file, if used (not usually relevant for GAMBLR)
unix_group: Whether a source is external and restricted by data access agreements (icgc_dart) or internal (gambl)
COO_consensus: TODO
DHITsig_consensus: TODO
COO_PRPS_class: TODO
DHITsig_PRPS_class: TODO
DLBCL90_dlbcl_call: TODO
DLBCL90_dhitsig_call: TODO
res_id: duplicate of sample_id for local samples and NA otherwise
DLBCL90_code_set: Code set used for DLBCL90 call. One of DLBCL90 DLBCL90v2 DLBCL90v3
DLBCL90_dlbcl_score: TODO
DLBCL90_pmbl_score: TODO
DLBCL90_pmbl_call: TODO
DLBCL90_dhitsig_score: TODO
myc_ba: Result from breakapart FISH for MYC locus
myc_cn: Result from copy number FISH for MYC locus
bcl2_ba: Result from breakapart FISH for BCL2 locus
bcl2_cn: Result from copy number FISH for BCL2 locus
bcl6_ba: Result from breakapart FISH for BCL6 locus
bcl6_cn: Result from copy number FISH for BCL6 locus
time_since_diagnosis_years: TODO
relapse_timing: TODO
dtbx: TODO. OR REMOVE?
dtdx: TODO. OR REMOVE?
lymphgen_no_cnv: TODO
lymphgen_with_cnv: TODO
lymphgen_cnv_noA53: TODO
lymphgen_wright: The LymphGen call for this sample from Wright et all (if applicable)
fl_grade: TODO
capture_frozen_sample_id: TODO
capture_FFPE_sample_id: TODO
capture_unknown_sample_id: TODO
genome_frozen_sample_id: TODO
genome_ctDNA_sample_id: TODO
genome_FFPE_sample_id: TODO
mrna_PolyA_frozen_sample_id: TODO
mrna_Ribodepletion_frozen_sample_id: TODO
mrna_Ribodepletion_frozen_sample_id: TODO
XXX_cohort: Cohort name for batch effect correction(?)
transformation: TODO
relapse: TODO
ighv_mutation_original: TODO
normal_sample_id: TODO
pairing_status: TODO
ICGC_ID: TODO
ICGC_XXX: metadata value for ICGC cohort inferred from external metadata
detailed_pathology: TODO
COO_final: TODO
consensus_pathology: TODO
lymphgen: TODO
Tumor_Sample_Barcode: Duplicate of sample_id for simplifying joins to MAF data frames
consensus_coo_dhitsig: TODO
pathology_rank: Numeric rank for consistent ordering of samples by pathology
lymphgen_rank: Numeric rank for consistent ordering of samples by LymphGen
hiv_status: TODO
CODE_XXX: Event-free status at last follow-up for overall survival (OS), progression-free survival (PFS) etc. 0 = no event/censored. 1 = event
XXX_YEARS: Time, in years, from diagnosis to last follow-up for overall survival (OS), progression-free survival (PFS)
alive: Theoretically redundant with CODE_OS
is_adult: Adult or pediatric at diagnosis. One of "Adult" for adults and "Pediatric" otherwise
age_group: Adult_BL or Pediatric_BL or Other, specific to the BLGSP study
age: patient age at diagnosis
sex: The biological sex of the patient, if available. Allowable options: M, F, NA
tx_primary: TODO
cause_of_death: TODO

Details

This function returns metadata for GAMBL samples. Options for subset and filter the returned data are available. For more information on how to use this function with different filtering criteria, refer to the parameter descriptions, examples and vignettes. Embargoed cases (current options: 'BLGSP-study', 'FL-study', 'DLBCL-study', 'FL-DLBCL-study', 'FL-DLBCL-all', 'DLBCL-unembargoed', 'BL-DLBCL-manuscript', 'MCL','MCL-CLL')

Examples

if (FALSE) { # \dontrun{
#basic usage
my_metadata = suppressMessages(get_gambl_metadata())

#use pre-defined custom sample sets
only_blgsp_metadata = get_gambl_metadata(case_set = "BLGSP-study")

#override default filters and request metadata for samples other than tumour genomes,
#e.g. also get the normals
tumour_and_normal_metadata = get_gambl_metadata(tissue_status_filter = c('tumour','normal'))

non_redundant_genome_and_capture = get_gambl_metadata(seq_type_filter = c('genome', 'capture'),
                                                       seq_type_priority = "genome")
                                                       
absolutely_everything = get_gambl_metadata(seq_type_filter = c('genome', 'capture','mrna'), tissue_status_filter=c('tumour','normal'))
} # }