DESCRIPTION

Package: lassie
Title: Tools to select sites and sequences that represent variation in a
    longitudinally sampled protein alignment
Version: 1.2
Authors@R: person("Peter", "Hraber", email="peterhraber@gmail.com", role=c("aut", "cre", "cph"))
Description: LASSIE is an acronym for "longitudinal antigenic sites and
    sequences from intrahost evolution" or "longitudinal antigenic swarm selection
    from intrahost evolution". It starts with a sequence alignment sampled serially
    from an infected host, which characterizes a pathogen population evolving under
    immune selection. The population is related by a single common "transmitted-
    founder" (TF) ancestor. The first phase of analysis computes TF loss per aligned
    site for each time-point sampled, to select sites of interest where TF loss
    exceeds a threshold. Sites that lose the ancestral TF amino acids are likely
    under positive selection and merit further investigation. The second phase
    selects a set of sequences with mutations among selected sites. A swarm of
    sequences represents diversity in the population sampled and can subsequently be
    used to study developing immune responses. Example data are included to identify
    sites on the HIV-1 envelope glycoprotein, to characterize affinity maturation
    which leads to a broadly neutralizing antibody response.
Depends:
    R (>= 3.1.1)
License: GPL-2
LazyData: true
Imports:
    seqinr
Suggests:
    knitr,
    devtools,
    binom,
    testthat
VignetteBuilder: knitr
RoxygenNote: 6.1.0
Encoding: UTF-8