Description Usage Arguments Value See Also Examples
Analyze longitudinal protein sequences for variants among selected sites.
1 2 3 |
ST |
swarmtools object, with list of selected sites. |
maxtol_deletion |
Maximum tolerated deletion length. |
maxtol_insertion |
Maximum tolerated insertion. |
included_clone_names |
List of included clone names. |
excluded_clone_names |
List of excluded clone names. |
min_counts |
Variants that occur less often than this number in the entire alignment are not included in swarms. The default value (2) catches all recurrent mutations. |
A swarmset object with selected sequences in a slot called
working_swarm
with values is_included==T
,
i.e. names(which(B$working_swarm$is_included))
.
Other swarmset methods: export.fasta.swarmset
,
export.swarmset
,
make.timepoint.logos
,
plot.swarmset
,
print.swarmset
,
resample.swarmset
,
summary.swarmset
,
tabulate.swarmset
1 2 3 4 5 6 | ## Not run:
A <- lassie::swarmtools(aas_file=system.file("extdata", "CH505-gp160.fasta",
package="lassie"), tf_loss_cutoff=80)
B <- lassie::swarmset(A)
## End(Not run)
|
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