Convert a panel/target table into PMO target_info + panel_info

Usage

pmo_panel_info_table_to_pmo(
  target_table,
  panel_name,
  genome_info = NULL,
  target_name_col = "target_name",
  forward_primers_seq_col = "fwd_primer",
  reverse_primers_seq_col = "rev_primer",
  reaction_name_col = NULL,
  reaction_name_col_delimiter = ",",
  forward_primers_start_col = NULL,
  forward_primers_end_col = NULL,
  reverse_primers_start_col = NULL,
  reverse_primers_end_col = NULL,
  insert_start_col = NULL,
  insert_end_col = NULL,
  chrom_col = NULL,
  strand_col = NULL,
  ref_seq_col = NULL,
  gene_name_col = NULL,
  genome_id_col = NULL,
  target_attributes_col = NULL,
  target_attributes_col_delimiter = ",",
  additional_target_info_cols = NULL
)

Arguments

target_table: A data.frame with one row per target.
panel_name: Name assigned to the panel.
genome_info: Optional genome metadata (a single genome list or a list of them); required if any location columns are used.
target_name_col, forward_primers_seq_col, reverse_primers_seq_col: Column names for the required fields.
reaction_name_col, reaction_name_col_delimiter: Optional reaction column (targets split into reactions); without it all targets form one full reaction.
forward_primers_start_col, forward_primers_end_col, reverse_primers_start_col, reverse_primers_end_col, insert_start_col, insert_end_col, chrom_col, strand_col, ref_seq_col: Optional genomic-location columns (0-based coordinates).
gene_name_col, genome_id_col, target_attributes_col, target_attributes_col_delimiter, additional_target_info_cols: Optional extra columns. genome_id_col values are 1-based; without it genome id defaults to 1.

Value

A list with panel_info, target_info, and (if genome_info given) targeted_genomes.

Examples

primers <- data.frame(target_name = c("t1", "t2"),
                      fwd_primer = c("AAAA", "CCCC"),
                      rev_primer = c("TTTT", "GGGG"))
panel <- pmo_panel_info_table_to_pmo(primers, "demo_panel")
length(panel$target_info)
#> [1] 2