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DESCRIPTION
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DESCRIPTION
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Package: seqmutprobs
Type: Package
Title: Screens sequence data for single-nucleotide site mutations-of-interest
Version: 1.0
Date: 2013-10-08
Author: TJ McKinley
Maintainer: TJ McKinley <tjm44@cam.ac.uk>
Description: This package compares sets of genetic sequences and screens for
nucleotide sites-of-interest, based on the methods developed in McKinley et
al., PLoS Comp. Biol. (2011) and McKinley et al. (2013), in preparation.
Depends:
seqinr (<= 3.5-0),
Rsamtools,
Rmpfr,
multicore,
ggplot2 (>= 0.9.3.1),
grid
SystemRequirements: samtools, Perl
License: GPL-3
LazyLoad: yes
Collate:
'calc_basedist.R'
'calc_cons.R'
'convert_align_pile.R'
'create_pileup.R'
'entropy.R'
'extract_site_info.R'
'gen_exact_norm.R'
'mutPPAs_top.R'
'mutlPDMs_full.R'
'num_to_char.R'
'plot_mutPPAs.R'
'plot_mutPPAs_list.R'
'plot_summary_mutPPAs.R'
'plot_summary_mutPPAs_list.R'
'print_mutPPAs.R'
'print_mutPPAs_list.R'
'print_summary_mutPPAs.R'
'print_summary_mutPPAs_list.R'
'seqtoPPAs.R'
'seqtoPPAs_default.R'
'subset_mutPPAs.R'
'summary_mutPPAS_list.R'
'summary_mutPPAs.R'
'mutPPAs_full.R'
'seqmutprobs-package.R'
'multiplot.R'
'plot_fullentropy.R'
'plot_sitesofinterest.R'