R: Subsetting Results

subsampler {Plasmidprofiler} | R Documentation

## 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)

[Package Plasmidprofiler version 0.1.6 Index]