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Parse a data frame with sample metadata

Source: R/pipeline.R
parse_sample_tab.Rd

Parse a data frame with sample metadata

Usage

parse_sample_tab(sample_tab)

Arguments

sample_tab

The sample table (data frame-like, see details)

Value

a valid sample metadata table (data frame) with sample names de-duplicated (if necessary)

Details

Required columns:

  • Plate

  • plate: A01-H12)

  • amplicon: forward-reverse, name as in 'primer_index' column of primer table; see parse_primer_tab

  • indexes: forward-reverse, name as in 'primer_index' column of primer table; see parse_primer_tab

  • sample: sample name, should not be duplicated

  • sample_type: Sample type such as 'negative control', will show up in reports; can be left empty

Optional columns:

  • taxon: Known or suspected taxon (any rank), will be compared to the sequence-based identification and used for detecting contamination

  • known sequence: Already known sequence (if any), e.g. from a previous Sanger sequencing; will be compared with the Nanopore-derived sequence

Note on amplicon multiplexing

Primers are searched in the order that amplicons appear in the sample table With nested amplicons, the shorter one should be placed at the end. Also place amplicons with little data before other amplicons with similar primers to make sure that they don't get "swallowed" in case of unspecific primer or sample index matching.