swarmset: Select sequences to represent mutations in selected sites.

Description Usage Arguments Value See Also Examples

Description

Analyze longitudinal protein sequences for variants among selected sites.

Usage

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swarmset(ST, maxtol_deletion = NULL, maxtol_insertion = NULL,
  included_clone_names = NULL, excluded_clone_names = NULL,
  min_counts = 2)

Arguments

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.

Value

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)).

See Also

swarmtools

Other swarmset methods: export.fasta.swarmset, export.swarmset, make.timepoint.logos, plot.swarmset, print.swarmset, resample.swarmset, summary.swarmset, tabulate.swarmset

Examples

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## 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)

phraber/lassie documentation built on May 25, 2019, 6:01 a.m.