.resolve_duplicates | R Documentation |
See 'select_unique_ngs' for details on selection criteria
.resolve_duplicates(x, data_cohort, oncotree_code, sample_type, min_max_time)
x |
sample ID to select unique NGS report for |
data_cohort |
output object of the create_analytic_cohort function. |
oncotree_code |
character vector specifying which sample OncoTree codes to keep. See "cpt_oncotree_code" column of data_cohort argument above to get options. |
sample_type |
character specifying which type of genomic sample to prioritize, options are "Primary", "Local" and "Metastasis". Default is to not select a NGS sample based on the sample type. |
min_max_time |
character specifying if the first or last genomic sample recorded should be kept. Options are "min" (first) and "max" (last). |
a dataframe of samples with one observation per patient.
nsclc_2_0 <- pull_data_synapse("NSCLC", version = "v2.0-public") ex1 <- create_analytic_cohort( data_synapse = nsclc_2_0$NSCLC_v2.0, stage_dx = c("Stage IV"), histology = "Adenocarcinoma" ) samples_data1 <- .resolve_duplicates( x = "GENIE-MSK-P-0025741", data_cohort = ex1$cohort_ngs, oncotree_code = "LUAD", sample_type = "Metastasis", min_max_time = "max" ) samples_data2 <- .resolve_duplicates( x = "GENIE-MSK-P-0025741", data_cohort = ex1$cohort_ngs, oncotree_code = "LUAD", sample_type = "Primary", min_max_time = "max" )
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