infer_from_combined {minSNPs}

infer_from_combined

Description

infer_from_combined infers the results (presence/absense of genes & CC) from the combined result

Usage

infer_from_combined(combined_result, search_table, genome_size, ...)

Arguments

combined_result

the combined result from combine_fastq_search_result or equivalent, with a list containing: - result: a dataframe containing the following columns: 'sequence', 'search_id', 'reads', 'raw_match', 'mean_qualities', 'indexes', 'id', 'type', 'strand', 'result', 'extra', 'match_ref_seq', 'n_reads' - read_length: 'reads_id', 'reads_length'

search_table

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

genome_size

estimated genome size for coverage calculation

...

additional arguments to pass to the process methods

Value

a dataframe containing the following columns: - type, rank, result, reads_count, proportion_matched, pass_filter