Create an Excel report

Usage

create_excel_report(
  seq_tab,
  outfile,
  low_abund_threshold = 20,
  min_seqs_unknown = 10,
  n_curate = 4,
  n_show_depth = 6,
  bam_dir = NULL
)

Arguments

seq_tab: data frame returned by do_assign_taxonomy
outfile: the Excel output file
low_abund_threshold: add 'low-coverage' to the issues list for samples with less reads
n_curate: max. number of sequences (polymorphism/haplotypes) from the top taxon to list in the curation section
n_show_depth: max. number of sequences (polymorphism/haplotypes) from the top taxon for which to output read numbers
bam_dir: Path to directory with separate BAM files (→ data link will appear). Relative hyperlinks are generated if bam_dir is a subdirectory of dirname(outfile), otherwise absolute paths are inserted, and moving the alignments directory will break the links.
min_seqs: ignore samples found in reads (index combination) but not in the samples table if they have less than the given number of reads