get_accepted_criteria: Get accepted criteria for different metrics

In AleSR13/refsampr: Making QC report from Reference Samples (analyzed with Juno pipeline)

Get accepted criteria for different metrics

Description

Get accepted criteria for different metrics

Usage

get_accepted_criteria(
  genus = character(),
  criterion = c("avg_phred", "Total length", "# contigs", "N50", "GC (%)",
    "Average coverage", "completeness", "contamination")
)

Arguments

genus	Character vector of length 1 with the name of a genus supported by the refsamp package. Currently accepted genera: "Bordetella", "Escherichia", "Listeria", "Neisseria", "Salmonella", "Shigella" and "Streptococcus".
criterion	Character vector of length 1 with one of the included quality criteria for acceptance of a sample. The currently accepted criteria are: "avg_phred", "Total length", "# contigs", "N50", "GC ( "Average coverage", "completeness" and "contamination".

Value

Dataframe of 2-3 rows (depending on the criterion) including the Genus and the yintercept or the Genus and the ymin and ymax for drawing a geom_hline or geom_rect, depending on the criterion.These are the thresholds to be used for accepting samples according to a$Run_date given quality criterion.

AleSR13/refsampr documentation built on May 30, 2022, 5:42 a.m.