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hyginn 2020-10-02 18:50:36 +10:00
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BIN-FUNC-Domain_annotation.R
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@ -3,18 +3,20 @@
# Purpose: A Bioinformatics Course:
# R code accompanying the BIN-FUNC-Domain_annotation unit.
#
# Version: 1.1
# Version: 1.2
#
# Date: 2017-11 - 2020-09
# Date: 2017-11 - 2020-10
# Author: Boris Steipe (boris.steipe@utoronto.ca)
#
# Versions:
# 1.2 Consistently: data in ./myScripts/ ;
# begin SHARING DATA section
# 1.1 2020 Updates
# 1.0 Live version 2017
# 0.1 First code copied from 2016 material.
#
# TODO:
#
# Complete SHARING DATA section ...
#
# == DO NOT SIMPLY source() THIS FILE! =======================================
#
@ -54,10 +56,10 @@
# IF YOU HAVE NOT YET COMPLETED THE BIN-ALI-OPTIMAL_SEQUENCE_ALIGNMENT UNIT:
#
# You DON'T already have a file called "<MYSPE>-Annotations.json" in the
# ./data/ directory:
# ./myScripts/ directory:
#
# - Make a copy of the file "./data/refAnnotations.json" and put it in your
# project directory.
# myScripts/ directory.
#
# - Give it a name that is structured like "<MYSPE>-Annotations.json" - e.g.
# if MYSPE is called "Crptycoccus neoformans", your file should be called
@ -79,15 +81,18 @@
# and change the "start" and "end" features to the coordinates you
# recorded in the SMART database.
#
# - Save your file.
# - Save your file in the ./myScripts/ folder.
#
# - Validate your file online at https://jsonlint.com/
#
# - Update your "makeProteinDB.R" script to load your new
# - Update your "./myScripts/makeProteinDB.R" script to load your new
# annotation when you recreate the database. Open the script in the
# RStudio editor, and add the following command at the end:
#
# myDB <- dbAddAnnotation(myDB, fromJSON("<MYSPE>-Annotations.json"))
# myDB <- dbAddAnnotation(myDB,
# jsonlite::fromJSON("./myScripts/<MYSPE>-Annotations.json"))
# ^^^^^^^
# edit this!
#
# - save and close the file.
#
@ -99,7 +104,7 @@
# IF YOU HAVE ALREADY COMPLETED THE BIN-ALI-OPTIMAL_SEQUENCE_ALIGNMENT UNIT:
#
# You SHOULD have a file called "<MYSPE>-Annotations.json" in the
# ./data/ directory:
# ./myScripts/ directory:
#
# - Open the file in the RStudio editor.
#
@ -109,7 +114,7 @@
# - Add a comma after every line except for the last one
#
# - Edit the annotations but include only features that are in the
# myDB$feature table. Check which features are in the databse by executing
# myDB$feature table. Check which features are in the database by executing
#
# myDB$feature$name
#
@ -125,7 +130,7 @@
#
# - source() your database creation script:
#
# source("makeProteinDB.R")
# source("./myScripts/makeProteinDB.R")
#
# This should run without errors or warnings. If it doesn't work and you
# can't figure out quickly what's happening, ask for help on the
@ -271,5 +276,16 @@ par(oPar) # reset the plot parameters
# It would be better to align the motif borders, at least approximately (not
# all proteins have all motifs). How would you go about doing that?
# = 1 SHARING DATA ======
# It's particularly interesting to compare such annotations across many
# homologous proteins. I have created a file on the student Wiki that you can
# edit, and then download the data from the entire class directly to your
# RStudio project.
#
# Task:
# =====
# Navigate to
# [END]