Google Sheets

Cohort-level tables are stored as public Google Sheets and are accessible directly as tibbles — no authentication or extra packages required.

get_metadata()

Returns a tibble with one row per sample and signature context, covering high-level cohort annotations.

meta <- get_metadata()
meta

Column	Description
SPN	SPN identifier (e.g. SPN01)
Sample	Sample identifier
FGA	Fraction of genome altered (High / Low)
FGS	Fraction of genome with SNVs (High / Low)
Clonal Class	Clonal architecture class
Clonal Subclass	Clonal architecture subclass
Tumour type	Tumour type abbreviation (e.g. CRC, AML)
Sample type	Multi-region or Longitudinal
Hypermutant Sample	Whether this sample is hypermutant
Hypermutant SPN	Whether the SPN as a whole is hypermutant
WGD	Whole-genome duplication detected
Signature Context	Mutational signature channel (e.g. SBS96, ID83)
Signature Class	Complexity class of the signature activity
Sex	Subject sex chromosome complement (e.g. XY, XX)

get_ground_truth_cna()

Returns a tibble of ground truth copy number segments. Can be filtered by SPN and/or sample.

get_ground_truth_cna()                          # all SPNs
get_ground_truth_cna("SPN01")                   # one SPN
get_ground_truth_cna("SPN01", sample = "1.1")   # one sample

Column	Description
SPN	SPN identifier
Sample	Sample identifier
Chromosome	Chromosome
Start	Segment start position
End	Segment end position
Major	Major allele copy number
minor	Minor allele copy number
CCF	Cancer cell fraction

get_ground_truth_drivers()

Returns a tibble of ground truth driver events (SNVs, CNAs, WGD). Can be filtered by SPN.

get_ground_truth_drivers()          # all SPNs
get_ground_truth_drivers("SPN01")   # one SPN

Column	Description
SPN	SPN identifier
mutant	Clone carrying the event
type	Event type (SID, CNA, WGD)
CNA_type	CNA subtype (e.g. D for deletion)
chr	Chromosome
start / end	Genomic coordinates
ref / alt	Reference and alternate alleles
code	Gene and amino acid change (e.g. APC R1450*)
allele	Affected allele
src_allele	Source allele

get_ground_truth_exposures()

Returns a tibble of ground truth mutational signature exposures. Can be filtered by SPN, sample, and/or signature type.

get_ground_truth_exposures()                          # all
get_ground_truth_exposures("SPN01")                   # one SPN
get_ground_truth_exposures("SPN01", type = "SBS")     # SBS only
get_ground_truth_exposures("SPN01", sample = "1.1")   # one sample

Column	Description
SPN	SPN identifier
Sample	Sample identifier
Coverage	Sequencing coverage
Purity	Sample purity
Type	Signature type (SBS, ID)
Signature	Signature name (e.g. SBS1, ID2)
Exposure	Signature exposure value

get_sampling_information()

Returns a tibble with per-sample sampling details including number of cells, sampling time, and clone proportions. Can be filtered by SPN and/or sample.

get_sampling_information()                        # all SPNs
get_sampling_information("SPN01")                 # one SPN
get_sampling_information("SPN01", sample = "1.1") # one sample

Column	Description
SPN	SPN identifier
Sample	Sample identifier
Number of cells	Number of sampled cells
Sampling time	Time of sampling
Clone 1–7 proportion	Proportion of each clone at sampling

read_sheet()

Generic reader for any public Google Sheet. Useful if you need to access additional tables not yet wrapped by a dedicated function.

df <- read_sheet(
  sheet_id = "<sheet_id>",
  gid      = "<tab_id>"
)

The sheet_id is the long string in the Google Sheets URL:

https://docs.google.com/spreadsheets/d/<sheet_id>/edit#gid=<gid>