Get all genetic data for a study or list of IDs

get_genetics(
  sample_ids = NULL,
  sample_list_id = NULL,
  genes = "all_impact",
  database = "msk_impact",
  mutations = TRUE,
  fusions = TRUE,
  cna = TRUE,
  seg = FALSE
)

Arguments

sample_ids

A character vector of sample ids

sample_list_id

A character vector naming a pre-specified list of samples (e.g. `"mskimpact_Colorectal_Cancer"`)

genes

A list of genes to query. default is all impact genes.

database

A character string of the database to be used. Options are "msk_impact" or "tcga", default is "msk_impact".

mutations

Boolean specifying if mutation data should be fetched. Default is TRUE.

fusions

Boolean specifying if fusion data should be fetched. Default is TRUE.

cna

Boolean specifying if cna data should be fetched. Default is TRUE.

seg

Boolean specifying if the segmentatio data should be fetched. Default is FALSE.

Value

A dataframe of mutations for each sample ID

Examples

if (FALSE) { # IMPACT # get_genetics(sample_ids = c("P-0000004-T01-IM3", "P-0000012-T02-IM3"), genes = 207) # TCGA # get_genetics(sample_ids = c("TCGA-17-Z023-01","TCGA-02-0003-01","TCGA-02-0055-01"), database = "tcga") }