process_snp_result {minSNPs}

process_snp_result

Description

process_snp_result processes the SNP result from infer_from_combined

Usage

process_snp_result(
  partial_result,
  search_table,
  count_measure = "n_reads",
  ...
)

Arguments

partial_result

the result from infer_from_combined with only SNP

search_table

a dataframe with the following columns: - "id","type","sequence","strand","result","extra","match_ref_seq"

count_measure

the column name of the count measure to use for removing the conflicts

...

ignored

Value

a list containing: - result: a dataframe containing the following columns: - type, rank, result, reads_count, proportion_matched, pass_filter, proportion_scheme_found, details - snps_found: a vector containing the SNPs ID that have been identified without conflict - proportion_snps_found: the proportion of SNPs found without conflict