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Removed 2021 Update warning

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This commit is contained in:
hyginn 2021-10-26 17:04:31 +02:00
parent 4b2bab0f12
commit 5e7b683323
7 changed files with 63 additions and 153 deletions
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24
BIN-ALI-BLAST.R
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@ -5,20 +5,6 @@
#
# ==============================================================================
#
# 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# of the code and data will change, and if you use this outdated code it will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
@ -46,13 +32,13 @@
#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> 1 Defining the APSES domain 45
#TOC> 2 Executing the BLAST search 75
#TOC> 3 Analysing results 97
#TOC>
#TOC> ==========================================================================

22
BIN-ALI-Dotplot.R
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@ -3,20 +3,6 @@
#
# ==============================================================================
#
# 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# of the code and data will change, and if you use this outdated code it will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.
#
@ -44,12 +30,12 @@
#TOC> ==========================================================================
#TOC>
#TOC>
#TOC> Section Title Line
#TOC> --------------------------------------
#TOC> 1 ___Section___ 39
#TOC> 2 Tasks 187
#TOC>
#TOC> 1 ___Section___ 42
#TOC> 2 Tasks 190
#TOC>
#TOC> ==========================================================================

21
BIN-ALI-MSA.R
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@ -3,21 +3,6 @@
# 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
@ -45,7 +30,7 @@
#TOC> ==========================================================================
#TOC>
#TOC>
#TOC> Section Title Line
#TOC> ------------------------------------------------------------------
#TOC> 1 Preparations 55
@ -63,7 +48,7 @@
#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> ==========================================================================
@ -256,7 +241,7 @@ 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)) {

40
BIN-ALI-Optimal_sequence_alignment.R
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@ -4,20 +4,6 @@
# 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
@ -52,20 +38,20 @@
#TOC> ==========================================================================
#TOC>
#TOC>
#TOC> Section Title Line
#TOC> --------------------------------------------------------------------------
#TOC> 1 Prepare 57
#TOC> 2 Biostrings Pairwise Alignment 74
#TOC> 2.1 Optimal global alignment 92
#TOC> 2.2 Optimal local alignment 155
#TOC> 3 APSES Domain annotation by alignment 179
#TOC> 4 Update your database script 260
#TOC> 4.1 Preparing an annotation file ... 266
#TOC> 4.1.1 If you HAVE NOT done the BIN-FUNC-Annotation unit 268
#TOC> 4.1.2 If you HAVE done the BIN-FUNC-Annotation unit 313
#TOC> 4.2 Execute and Validate 337
#TOC>
#TOC> 1 Prepare 58
#TOC> 2 Biostrings Pairwise Alignment 75
#TOC> 2.1 Optimal global alignment 93
#TOC> 2.2 Optimal local alignment 156
#TOC> 3 APSES Domain annotation by alignment 180
#TOC> 4 Update your database script 261
#TOC> 4.1 Preparing an annotation file ... 267
#TOC> 4.1.1 If you HAVE NOT done the BIN-FUNC-Annotation unit 269
#TOC> 4.1.2 If you HAVE done the BIN-FUNC-Annotation unit 314
#TOC> 4.2 Execute and Validate 338
#TOC>
#TOC> ==========================================================================
@ -325,7 +311,7 @@ aliApses@subject@range@start + aliApses@subject@range@width - 1
# Then SKIP the next section.
#
#
# === 4.1.2 If you HAVE done the BIN-FUNC-Annotation unit
# === 4.1.2 If you HAVE done the BIN-FUNC-Annotation unit
#
#
# You DO already have a file called "<MYSPE>-Annotations.json" in the

38
BIN-FUNC-Domain_annotation.R
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@ -4,20 +4,6 @@
# 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
@ -46,19 +32,19 @@
#TOC> ==========================================================================
#TOC>
#TOC>
#TOC> Section Title Line
#TOC> ---------------------------------------------------------------------
#TOC> 1 Update your database script 50
#TOC> 1.1 Preparing an annotation file ... 57
#TOC> 1.1.1 BEFORE "BIN-ALI-Optimal_sequence_alignment" 60
#TOC> 1.1.2 AFTER "BIN-ALI-Optimal_sequence_alignment" 108
#TOC> 1.2 Execute and Validate 135
#TOC> 2 Plot Annotations 160
#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> 1 Update your database script 51
#TOC> 1.1 Preparing an annotation file ... 58
#TOC> 1.1.1 BEFORE "BIN-ALI-Optimal_sequence_alignment" 61
#TOC> 1.1.2 AFTER "BIN-ALI-Optimal_sequence_alignment" 109
#TOC> 1.2 Execute and Validate 136
#TOC> 2 Plot Annotations 161
#TOC> 3 SHARING DATA 287
#TOC> 3.1 Post MBP1_MYSPE as JSON data 303
#TOC> 3.2 Import shared MBP1_MYSPE from the Wiki 326
#TOC>
#TOC> ==========================================================================
@ -120,7 +106,7 @@
# 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:
#

24
FND-STA-Information_theory.R
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@ -2,20 +2,6 @@
#
# ==============================================================================
#
# 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.
#
@ -42,8 +28,16 @@
# ==============================================================================
#TOC> ==========================================================================
#TOC>
#TOC> Section Title Line
#TOC> --------------------------------------
#TOC> 1 ___Section___ 39
#TOC>
#TOC> ==========================================================================
# = 1 ___Section___
# = 1 ___Section___ =======================================================
# What level of information is "significant"

47
RPR-GEO2R.R
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@ -1,24 +1,10 @@
# tocID <- "RPR_GEO2R.R"
# tocID <- "RPR-GEO2R.R"
#
# 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
@ -53,22 +39,23 @@
#TOC> ==========================================================================
#TOC>
#TOC>
#TOC> Section Title Line
#TOC> --------------------------------------------------------------------------
#TOC> 1 Preparations 56
#TOC> 2 Loading a GEO Dataset 82
#TOC> 3 Column wise analysis - time points 152
#TOC> 3.1 Task - Comparison of experiments 158
#TOC> 3.2 Grouped Samples 205
#TOC> 4 Row-wise Analysis: Expression Profiles 240
#TOC> 4.1 Task - Read a table of features 275
#TOC> 4.2 Selected Expression profiles 323
#TOC> 5 Differential Expression 364
#TOC> 5.1 Final task: Gene descriptions 504
#TOC> 6 Improving on Discovery by Differential Expression 510
#TOC> 7 Annotation data 594
#TOC>
#TOC> 1 Preparations 62
#TOC> 2 Loading a GEO Dataset 89
#TOC> 2.1 Task - understanding the data 155
#TOC> 3 Column wise analysis - time points 164
#TOC> 3.1 Task - Comparison of experiments 193
#TOC> 3.2 Grouped Samples 226
#TOC> 4 Row-wise Analysis: Expression Profiles 261
#TOC> 4.1 Task - Read a table of features 296
#TOC> 4.2 Selected Expression profiles 349
#TOC> 5 Differential Expression 392
#TOC> 5.1 Final task: Gene descriptions 532
#TOC> 6 Improving on Discovery by Differential Expression 538
#TOC> 7 Annotation data 633
#TOC>
#TOC> ==========================================================================
@ -165,7 +152,7 @@ Biobase::sampleNames(GSE3635)[1:10] # Columns. What are these columns?
# Access data
Biobase::exprs(tmp) # exprs() gives us the actual expression values.
# == 3.1 Task - understanding the data ==================================
# == 2.1 Task - understanding the data =====================================
#TASK> What are the data values:
#TASK> ... in each cell?