subsampler {Plasmidprofiler}

Subsetting Results

Description

Several filters can be applied:
   Coverage: Filters results below percent read coverage specified
               eg. 95.9 cuts results where reads covered less than 95.9% of the total length
   Sureness: Filters results below sureness specified
               eg. 0.9 cuts results where the sureness falls below 0.9
   Length:   Filters plasmid sequences shorter than length specified
               eg. 10000 cuts out results where the plasmid was less than 10kb
   Incompatibility groups can also be combined (eg. Fii(S) and Fii(K) are combined into Fii)

Usage

subsampler(report, cov.filter = NA, sure.filter = NA, len.filter = NA,
  inc.combine = NA)

Arguments

report

Dataframe of results produced by subsampler or combine_results

cov.filter

Filters results below percent read coverage specified (eg. 80)

sure.filter

Filters results below sureness specified (eg. 0.75)

len.filter

Filters plasmid sequences shorter than length specified (eg. 10000)

inc.combine

Flag to ombine incompatibility sub-groups into their main type (set to 1)

Value

Report with filters applied

See Also

subsampler, combine_results

Examples

## Not run: 
subsampler(report, sureness.filter = 0.75, len.filter = 10000)

## End(Not run)