Build minimal library/specimen info from a detected-microhaplotypes structure

Usage

pmo_minimum_library_specimen_from_mhap_table(
  detected_microhaps,
  panel_name,
  library_sample_specimen_key = NULL,
  library_sample_name_col = "library_sample_name",
  specimen_name_col = "specimen_name",
  missing_library_sample_becomes_specimen_name = FALSE
)

Arguments

detected_microhaps: The list of detected-microhaplotype sets (the detected_microhaplotypes element from pmo_mhap_table_to_pmo()).
panel_name: Panel name to assign to each library sample.
library_sample_specimen_key: Optional named character vector or data.frame mapping library sample name to specimen name; if NULL, specimen name equals library sample name.
library_sample_name_col, specimen_name_col: Column names used when library_sample_specimen_key is a data.frame.
missing_library_sample_becomes_specimen_name: If TRUE, library samples absent from the key fall back to using their own name as the specimen name.

Value

A list with library_sample_info and specimen_info.

Examples

calls <- data.frame(library_sample_name = c("S1", "S2"),
                    target_name = c("t1", "t1"), seq = c("ACGT", "ACGA"),
                    reads = c(120, 95))
mhaps <- pmo_mhap_table_to_pmo(calls)
ls <- pmo_minimum_library_specimen_from_mhap_table(
  mhaps$detected_microhaplotypes, panel_name = "demo_panel")
length(ls$specimen_info)
#> [1] 2