114 lines
3.6 KiB
R
114 lines
3.6 KiB
R
# ___ID___ .R
|
|
#
|
|
# Purpose: A Bioinformatics Course:
|
|
# R code accompanying the ___ID___ unit.
|
|
#
|
|
# Version: 0.1
|
|
#
|
|
# Date: 2017 08 28
|
|
# Author: Boris Steipe (boris.steipe@utoronto.ca)
|
|
#
|
|
# Versions:
|
|
# 0.1 First code copied from 2016 material.
|
|
|
|
#
|
|
# TODO:
|
|
#
|
|
#
|
|
# == DO NOT SIMPLY source() THIS FILE! =======================================
|
|
|
|
# If there are portions you don't understand, use R's help system, Google for an
|
|
# answer, or ask your instructor. Don't continue if you don't understand what's
|
|
# going on. That's not how it works ...
|
|
|
|
# ==============================================================================
|
|
|
|
# = 1 ___Section___
|
|
|
|
# ==============================================================================
|
|
# PART FOUR: Calculating trees
|
|
# ==============================================================================
|
|
|
|
# Follow the instructions found at phylip's home on the Web to install. If you
|
|
# are on a Windows computer, take note of the installation directory.
|
|
|
|
# After you have installed Phylip on your computer, install the R package that
|
|
# provides an interface to the Phylip functions.
|
|
|
|
if (!require(Rphylip, quietly=TRUE)) {
|
|
install.packages("Rphylip")
|
|
library(Rphylip)
|
|
}
|
|
|
|
# This will install RPhylip, as well as its dependency, the package "ape".
|
|
|
|
# The next part may be tricky. You will need to figure out where
|
|
# on your computer Phylip has been installed and define the path
|
|
# to the proml program that calculates a maximum-likelihood tree.
|
|
|
|
# On the Mac, the standard installation places a phylip folder
|
|
# in the /Applications directory. That folder contains all the
|
|
# individual phylip programs as <name>.app files. These are not
|
|
# the actual executables, but "app" files are actually directories
|
|
# that contain the required resources for a program to run.
|
|
|
|
# The executable is in a subdirectory and you can point Rphylip
|
|
# directly to that subdirectory to find the program it needs:
|
|
# PROMLPATH <- "/Applications/phylip-3.695/exe/proml.app/Contents/MacOS"
|
|
|
|
# On Windows you need to know where the rograms have been installed, and you
|
|
# need to specify a path that is correct for the Windows OS. Find the folder
|
|
# that is named "exe", and right-click to inspect its properties. The path
|
|
# should be listed among them.
|
|
|
|
# If the path looks like "C:\Users\Meng\Programs\phylip-3.695\exe", then your
|
|
# assignment has to be
|
|
# PROMLPATH <- "C:/Users/Meng/Programs/phylip-3.695/exe"
|
|
# (Note: "/", not "\")
|
|
|
|
# I have heard that your path must not contain spaces, and it is prudent to
|
|
# avoid other special characters as well.
|
|
|
|
# If you are running Linux I trust you know what to do. It's probably
|
|
# something like
|
|
# PROMLPATH <- "/usr/local/phylip-3.695/bin"
|
|
|
|
# Confirm that the settings are right.
|
|
PROMLPATH # returns the path
|
|
list.dirs(PROMLPATH) # returns the directories in that path
|
|
list.files(PROMLPATH) # lists the files
|
|
|
|
# If "proml" is NOT among the files that the last command returns, you
|
|
# can't continue.
|
|
|
|
# Now read the mfa file you have saved, as a "proseq" object with the
|
|
# read.protein() function of the RPhylip package:
|
|
|
|
apsIn <- read.protein("APSES.mfa")
|
|
apsIn <- read.protein("~/Desktop/APSES_HISCA.mfa")
|
|
|
|
# ... and you are ready to build a tree.
|
|
|
|
# Building maximum-likelihood trees can eat as much computer time
|
|
# as you can throw at it. Calculating a tree of 48 APSES domains
|
|
# with default parameters of Rproml() runs for more than half a day
|
|
# on my computer. But we have only twelve sequences here, so the
|
|
# process will take us about 5 to 10 minutes.
|
|
|
|
apsTree <- Rproml(apsIn, path=PROMLPATH)
|
|
|
|
|
|
|
|
# A quick first look:
|
|
|
|
plot(apsTree)
|
|
|
|
|
|
|
|
# = 1 Tasks
|
|
|
|
|
|
|
|
|
|
# [END]
|