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 )
sample_ids | A character vector of sample ids |
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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. |
A dataframe of mutations for each sample ID