Description Usage Arguments Value See Also Examples
1 2 3 4 5 6 7 8 | 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)
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1 2 |
report |
Dataframe of results produced
by |
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) |
Report with filters applied
1 2 3 4 | ## Not run:
subsampler(report, sureness.filter = 0.75, len.filter = 10000)
## End(Not run)
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