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Locked out - Updates needed for 2021

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hyginn 2021-09-16 01:29:19 -04:00
parent 2956ba29b5
commit 9143b784e9
8 changed files with 139 additions and 21 deletions
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20
BIN-ALI-BLAST.R
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@ -3,6 +3,22 @@
# Purpose: A Bioinformatics Course:
# R code accompanying the BIN-ALI-BLAST unit.
#
# ==============================================================================
#
# S T O P :
# =========
#
# 2021
# UPDATE WARNING!
# ---------------
#
# This file has not yet been updated for coursework. You may inspect it, but
# do NOT use it for actual coursework as long as this warning is here. Parts
# of the code and data will change, and if you use this outdated code it will
# break your setup and workflow.
#
# ==============================================================================
#
# Version: 1.3
#
# Date: 2017-10 - 2020-09
@ -30,13 +46,13 @@
#TOC> ==========================================================================
#TOC>
#TOC>
#TOC> Section Title Line
#TOC> ---------------------------------------------------
#TOC> 1 Defining the APSES domain 43
#TOC> 2 Executing the BLAST search 73
#TOC> 3 Analysing results 95
#TOC>
#TOC>
#TOC> ==========================================================================

21
BIN-ALI-Dotplot.R
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@ -1,10 +1,21 @@
# tocID <- "BIN-ALI-Dotplot.R"
#
# ---------------------------------------------------------------------------- #
# PATIENCE ... #
# Do not yet work wih this code. Updates in progress. Thank you. #
# boris.steipe@utoronto.ca #
# ---------------------------------------------------------------------------- #
#
# ==============================================================================
#
# S T O P :
# =========
#
# 2021
# UPDATE WARNING!
# ---------------
#
# This file has not yet been updated for coursework. You may inspect it, but
# do NOT use it for actual coursework as long as this warning is here. Parts
# of the code and data will change, and if you use this outdated code it will
# break your setup and workflow.
#
# ==============================================================================
#
# Purpose: A Bioinformatics Course:
# R code accompanying the BIN-ALI-Dotplot unit.

21
BIN-ALI-MSA.R
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@ -3,6 +3,21 @@
# Purpose: A Bioinformatics Course:
# R code accompanying the BIN-ALI-MSA unit.
#
# ==============================================================================
#
# S T O P :
# =========
#
# 2021
# UPDATE WARNING!
# ---------------
#
# This file has not yet been updated for coursework. You may inspect it, but
# do NOT use it for actual coursework as long as this warning is here. Parts
# of the code and data will change, and if you use this outdated code it will
# break your setup and workflow.
#
# ==============================================================================
# Version: 1.3
#
# Date: 2017-10 - 2020-09
@ -30,7 +45,7 @@
#TOC> ==========================================================================
#TOC>
#TOC>
#TOC> Section Title Line
#TOC> ------------------------------------------------------------------
#TOC> 1 Preparations 55
@ -48,7 +63,7 @@
#TOC> 6 Sequence Logos 549
#TOC> 6.1 Subsetting an alignment by motif 558
#TOC> 6.2 Plot a Sequence Logo 607
#TOC>
#TOC>
#TOC> ==========================================================================
@ -241,7 +256,7 @@ for (i in seq_along(highScoringRanges$lengths)) {
# - adjust the sequence names
# - convert to msaAAMultipleAlignment object
# === 4.1.1 importing an .aln file
# === 4.1.1 importing an .aln file
# The seqinr package has a function to read CLUSTAL W formatted .aln files ...
if (! requireNamespace("seqinr", quietly=TRUE)) {

15
BIN-ALI-Optimal_sequence_alignment.R
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@ -3,6 +3,21 @@
# Purpose: A Bioinformatics Course:
# R code accompanying the BIN-ALI-Optimal_sequence_alignment unit.
#
# ==============================================================================
#
# S T O P :
# =========
#
# 2021
# UPDATE WARNING!
# ---------------
#
# This file has not yet been updated for coursework. You may inspect it, but
# do NOT use it for actual coursework as long as this warning is here. Parts
# of the code and data will change, and if you use this outdated code it will
# break your setup and workflow.
#
# ==============================================================================
# Version: 1.7.1
#
# Date: 2017-09 - 2020-10

21
BIN-FUNC-Domain_annotation.R
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@ -3,6 +3,21 @@
# Purpose: A Bioinformatics Course:
# R code accompanying the BIN-FUNC-Domain_annotation unit.
#
# ==============================================================================
#
# S T O P :
# =========
#
# 2021
# UPDATE WARNING!
# ---------------
#
# This file has not yet been updated for coursework. You may inspect it, but
# do NOT use it for actual coursework as long as this warning is here. Parts
# of the code and data will change, and if you use this outdated code it will
# break your setup and workflow.
#
# ==============================================================================
# Version: 1.4
#
# Date: 2017-11 - 2020-10
@ -31,7 +46,7 @@
#TOC> ==========================================================================
#TOC>
#TOC>
#TOC> Section Title Line
#TOC> ---------------------------------------------------------------------
#TOC> 1 Update your database script 50
@ -43,7 +58,7 @@
#TOC> 3 SHARING DATA 286
#TOC> 3.1 Post MBP1_MYSPE as JSON data 302
#TOC> 3.2 Import shared MBP1_MYSPE from the Wiki 325
#TOC>
#TOC>
#TOC> ==========================================================================
@ -105,7 +120,7 @@
# Then SKIP the next section.
#
#
# === 1.1.2 AFTER "BIN-ALI-Optimal_sequence_alignment"
# === 1.1.2 AFTER "BIN-ALI-Optimal_sequence_alignment"
#
# IF YOU HAVE ALREADY COMPLETED THE BIN-ALI-OPTIMAL_SEQUENCE_ALIGNMENT UNIT:
#

21
BIN-MYSPE.R
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@ -3,6 +3,23 @@
# Purpose: A Bioinformatics Course:
# R code accompanying the BIN-MYSPE unit
#
# ==============================================================================
#
# S T O P :
# =========
#
# 2021
# UPDATE WARNING!
# ---------------
#
# This file has not yet been updated for coursework. You may inspect it, but
# do NOT use it for actual coursework as long as this warning is here. Parts
# of the code and data will change, and if you use this outdated code it will
# break your setup and workflow.
#
# ==============================================================================
#
#
# Version: 1.2
#
# Date: 2020-10-01
@ -31,7 +48,7 @@
#TOC> ==========================================================================
#TOC>
#TOC>
#TOC> Section Title Line
#TOC> -----------------------------------------------------------------
#TOC> 1 PREPARATIONS 49
@ -42,7 +59,7 @@
#TOC> 4.2 Visualizing proportions: Pie chart 161
#TOC> 4.3 Visualizing proportions: Nested squares 238
#TOC> 4.4 Visualizing proportions: Sankey diagrams 275
#TOC>
#TOC>
#TOC> ==========================================================================

22
FND-STA-Information_theory.R
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@ -1,17 +1,27 @@
# tocID <- "FND-STA-Information_theory.R"
#
# ---------------------------------------------------------------------------- #
# PATIENCE ... #
# Do not yet work wih this code. Updates in progress. Thank you. #
# boris.steipe@utoronto.ca #
# ---------------------------------------------------------------------------- #
# ==============================================================================
#
# S T O P :
# =========
#
# 2021
# UPDATE WARNING!
# ---------------
#
# This file has not yet been updated for coursework. You may inspect it, but
# do NOT use it for actual coursework as long as this warning is here. Parts
# of the code and data will change, and if you use this outdated code it will
# break your setup and workflow.
#
# ==============================================================================
#
# Purpose: A Bioinformatics Course:
# R code accompanying the FND-STA-Information_theory unit.
#
# Version: 0.2.1
#
# Date: 2017 - 2019
# Date: 2017 - 2021
# Author: Boris Steipe (boris.steipe@utoronto.ca)
#
# Versions:

19
RPR-GEO2R.R
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@ -3,6 +3,22 @@
# Purpose: A Bioinformatics Course:
# R code accompanying the RPR_GEO2R unit.
#
#
# ==============================================================================
#
# S T O P :
# =========
#
# 2021
# UPDATE WARNING!
# ---------------
#
# This file has not yet been updated for coursework. You may inspect it, but
# do NOT use it for actual coursework as long as this warning is here. Parts
# of the code and data will change, and if you use this outdated code it will
# break your setup and workflow.
#
# ==============================================================================
# Version: 1.3
#
# Date: 2017-09 - 2020-09
@ -292,6 +308,9 @@ readLines("./data/SGD_features.tab", n = 5)
# == 4.1 Task - Read a table of features ===================================
# Note: this task asks you to write code. You MUST identify your
# sources when you draw on other's examples.
# This data file is rather typical of datasets that you will encounter "in the
# wild". To proceed, you need to write code to read it into an R-object. Develop
# the code in your script file according to the following specification: