Get GAMBL Metadata.
get_gambl_metadata.RdConvenience function for loading the sample metadata.
Usage
get_gambl_metadata(seq_type_filter = c("genome", "capture"), case_set, ...)Value
A data frame with metadata, tailored for user without GSC access.
- 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.
- cohort
Name for a group of samples that were added together (usually from a single study), often in the format pathology_cohort_descriptor.
- pathology
The diagnosis or pathology for the sample
- time_point
Timing of biopsy in increasing alphabetical order (A = diagnosis, B = first relapse etc)
- ffpe_or_frozen
Whether the nucleic acids were extracted from a frozen or FFPE sample
- COO_consensus
Consensus call of COO between different sources.
- DHITsig_consensus
Consensus call of DHIT signature status between different sources.
- EBV_status_inf
Inferred EBV status of the tumor
- lymphgen_no_cnv
LymphGen label using model without CNV
- lymphgen_with_cnv
LymphGen label using model with CNV
- lymphgen_cnv_noA53
LymphGen label using model with CNV but excluding A53 class
- lymphgen_wright
The LymphGen call for this sample from Wright et all (if applicable)
- fl_grade
Grade of FL samples
- normal_sample_id
Sample id for normal tissue used in the analysis
- pairing_status
Matching status of the sample
- lymphgen
LymphGen label
- molecular_BL
label of the sample according to the molecular BL classifier
- Tumor_Sample_Barcode
Duplicate of sample_id for simplifying joins to MAF data frames
- pathology_rank
Numeric rank for consistent ordering of samples by pathology
- hiv_status
HIV status of the sample
- age_group
Adult_BL or Pediatric_BL or Other, specific to the BLGSP study
- sex
The biological sex of the patient, if available. Allowable options: M, F, NA
Details
This bare bones function was developed to retrieve metadata for
non-GSC-users. Specify the seq type (seq_type_filter) for the samples you
want returned as the only argument.
It relies on the bundled metadata in this package.
Specify case_set argument to retreive samples from particular study.
Currently supported case_sets are: FL_Dreval (FL samples from Dreval et al),
DLBCL_Dreval (DLBCL samples from Dreval et al), FL-DLBCL-study (all samples
from Dreval et al), DLBCL_Arthur (all samples from Arthur et al study),
DLBCL_Hilton (all samples from Hilton et al DLBCL Trios study),
DLBCL_cell_lines (5 DLBCL cell lines), DLBCL_Chapuy (all samples from Chapuy
et al study), DLBCL_Schmitz (all samples from Schmitz et al study),
DLBCL_Reddy (all samples from Reddy et al study), DLBCL_Thomas (HTMCP DLBCLs
from Thomas et al study), BL_Thomas (BL samples from Thomas et al study)
Examples
#return metadata for genome samples (here, the parameter is redundant because 'genome' is the default)
genome_meta = get_gambl_metadata(seq_type_filter = "genome")
#> Using the bundled metadata in GAMBLR.data...
#return metadata for capture samples.
capture_meta = get_gambl_metadata(seq_type_filter = "capture")
#> Using the bundled metadata in GAMBLR.data...
#If you want metadata for genome and capture samples you can provide a vector of seq types
all_meta = get_gambl_metadata(seq_type_filter = c("genome", "capture"))
#> Using the bundled metadata in GAMBLR.data...
dplyr::group_by(all_meta,cohort,seq_type) %>%
dplyr::count()
#> # A tibble: 21 × 3
#> # Groups: cohort, seq_type [21]
#> cohort seq_type n
#> <chr> <chr> <int>
#> 1 BL_Adult genome 91
#> 2 BL_Pediatric genome 121
#> 3 BL_cell_lines genome 22
#> 4 DLBCL_Gascoyne genome 21
#> 5 DLBCL_GenomeCanada genome 59
#> 6 DLBCL_HTMCP genome 43
#> 7 DLBCL_ICGC genome 84
#> 8 DLBCL_LSARP_Trios capture 12
#> 9 DLBCL_LSARP_Trios genome 142
#> 10 DLBCL_Marra genome 38
#> # ℹ 11 more rows