In phraber/lassie: Tools to select sites and sequences that represent variation in a longitudinally sampled protein alignment

Phase I: Select Sites

This phase of analysis requires:

1. A protein alignment, provisionally assumed to be in FASTA format.
2. A way to recognize how the longitudinal samples are labeled.
   By default, sequence names are assumed to be dot-delimited, with the timepoint label in the first (left-most) field.
3. An indication of which sequence is the reference/TF sequence.
   By default, this is taken to be the first sequence in the alignment.

Choose a Cutoff Setting

We need to choose a setting for the cutoff parameter value. Let's see how number of sites depends on cutoff threshold. A vector of cutoff values shows how many sites result from multiple settings. Note that the default values work for these data.

In practice, you will not need to use system.file() unless you are referring to an example alignment included with the swarmtools package.

    library(lassie)
    alignment_file <- system.file("extdata", "CH505-gp160.fasta", package="lassie")
    eg.swarmtools <- swarmtools(aas_file=alignment_file, tf_loss_cutoff=80)
    summary(eg.swarmtools)
    plot(eg.swarmtools)
    print(eg.swarmtools)

The 80% cutoff value gives 35 sites. Let's go with that.

Phase II: Select Clones

This phase of analysis requires a SwarmTools object created in Phase I.
The SwarmTools object must have a list of selected sites, which happens only when it was created using a single tf_loss_cutoff value. Let's just go with the defaults.

eg.swarmset <- swarmset(eg.swarmtools)

All Together Now

Got that? Here's the whole workflow:

    library(lassie)
    alignment_file <- system.file("extdata", "CH505-gp160.fasta", package="lassie")
    eg.swarmtools <- swarmtools(aas_file=alignment_file, tf_loss_cutoff=80)
    summary(eg.swarmtools)
    print(eg.swarmtools)
    eg.swarmset <- swarmset(eg.swarmtools)
    summary(eg.swarmset)
    print(eg.swarmset)
    plot(eg.swarmset)

For some fun advanced plotting routines, try running lassie::report.variant.frequencies(eg.swarmtools) and lassie::make.timepoint.logos(eg.swarmset).

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