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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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20
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# of the code and data will change, and if you use this outdated code it will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 # Version: 1.3
# #
# Date: 2017-10 - 2020-09 # Date: 2017-10 - 2020-09
@ -49,9 +35,9 @@
#TOC> #TOC>
#TOC> Section Title Line #TOC> Section Title Line
#TOC> --------------------------------------------------- #TOC> ---------------------------------------------------
#TOC> 1 Defining the APSES domain 43 #TOC> 1 Defining the APSES domain 45
#TOC> 2 Executing the BLAST search 73 #TOC> 2 Executing the BLAST search 75
#TOC> 3 Analysing results 95 #TOC> 3 Analysing results 97
#TOC> #TOC>
#TOC> ========================================================================== #TOC> ==========================================================================

18
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# of the code and data will change, and if you use this outdated code it will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: # Purpose: A Bioinformatics Course:
# R code accompanying the BIN-ALI-Dotplot unit. # R code accompanying the BIN-ALI-Dotplot unit.
# #
@ -47,8 +33,8 @@
#TOC> #TOC>
#TOC> Section Title Line #TOC> Section Title Line
#TOC> -------------------------------------- #TOC> --------------------------------------
#TOC> 1 ___Section___ 39 #TOC> 1 ___Section___ 42
#TOC> 2 Tasks 187 #TOC> 2 Tasks 190
#TOC> #TOC>
#TOC> ========================================================================== #TOC> ==========================================================================

15
BIN-ALI-MSA.R
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@ -3,21 +3,6 @@
# Purpose: A Bioinformatics Course: # Purpose: A Bioinformatics Course:
# R code accompanying the BIN-ALI-MSA unit. # 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 # Version: 1.3
# #
# Date: 2017-10 - 2020-09 # Date: 2017-10 - 2020-09

34
BIN-ALI-Optimal_sequence_alignment.R
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@ -4,20 +4,6 @@
# R code accompanying the BIN-ALI-Optimal_sequence_alignment unit. # 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 # Version: 1.7.1
# #
# Date: 2017-09 - 2020-10 # Date: 2017-09 - 2020-10
@ -55,16 +41,16 @@
#TOC> #TOC>
#TOC> Section Title Line #TOC> Section Title Line
#TOC> -------------------------------------------------------------------------- #TOC> --------------------------------------------------------------------------
#TOC> 1 Prepare 57 #TOC> 1 Prepare 58
#TOC> 2 Biostrings Pairwise Alignment 74 #TOC> 2 Biostrings Pairwise Alignment 75
#TOC> 2.1 Optimal global alignment 92 #TOC> 2.1 Optimal global alignment 93
#TOC> 2.2 Optimal local alignment 155 #TOC> 2.2 Optimal local alignment 156
#TOC> 3 APSES Domain annotation by alignment 179 #TOC> 3 APSES Domain annotation by alignment 180
#TOC> 4 Update your database script 260 #TOC> 4 Update your database script 261
#TOC> 4.1 Preparing an annotation file ... 266 #TOC> 4.1 Preparing an annotation file ... 267
#TOC> 4.1.1 If you HAVE NOT done the BIN-FUNC-Annotation unit 268 #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 313 #TOC> 4.1.2 If you HAVE done the BIN-FUNC-Annotation unit 314
#TOC> 4.2 Execute and Validate 337 #TOC> 4.2 Execute and Validate 338
#TOC> #TOC>
#TOC> ========================================================================== #TOC> ==========================================================================

32
BIN-FUNC-Domain_annotation.R
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@ -4,20 +4,6 @@
# R code accompanying the BIN-FUNC-Domain_annotation unit. # 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 # Version: 1.4
# #
# Date: 2017-11 - 2020-10 # Date: 2017-11 - 2020-10
@ -49,15 +35,15 @@
#TOC> #TOC>
#TOC> Section Title Line #TOC> Section Title Line
#TOC> --------------------------------------------------------------------- #TOC> ---------------------------------------------------------------------
#TOC> 1 Update your database script 50 #TOC> 1 Update your database script 51
#TOC> 1.1 Preparing an annotation file ... 57 #TOC> 1.1 Preparing an annotation file ... 58
#TOC> 1.1.1 BEFORE "BIN-ALI-Optimal_sequence_alignment" 60 #TOC> 1.1.1 BEFORE "BIN-ALI-Optimal_sequence_alignment" 61
#TOC> 1.1.2 AFTER "BIN-ALI-Optimal_sequence_alignment" 108 #TOC> 1.1.2 AFTER "BIN-ALI-Optimal_sequence_alignment" 109
#TOC> 1.2 Execute and Validate 135 #TOC> 1.2 Execute and Validate 136
#TOC> 2 Plot Annotations 160 #TOC> 2 Plot Annotations 161
#TOC> 3 SHARING DATA 286 #TOC> 3 SHARING DATA 287
#TOC> 3.1 Post MBP1_MYSPE as JSON data 302 #TOC> 3.1 Post MBP1_MYSPE as JSON data 303
#TOC> 3.2 Import shared MBP1_MYSPE from the Wiki 325 #TOC> 3.2 Import shared MBP1_MYSPE from the Wiki 326
#TOC> #TOC>
#TOC> ========================================================================== #TOC> ==========================================================================

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: # Purpose: A Bioinformatics Course:
# R code accompanying the FND-STA-Information_theory unit. # 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" # What level of information is "significant"

43
RPR-GEO2R.R
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@ -1,24 +1,10 @@
# tocID <- "RPR_GEO2R.R" # tocID <- "RPR-GEO2R.R"
# #
# Purpose: A Bioinformatics Course: # Purpose: A Bioinformatics Course:
# R code accompanying the RPR_GEO2R unit. # 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 # Version: 1.3
# #
# Date: 2017-09 - 2020-09 # Date: 2017-09 - 2020-09
@ -56,18 +42,19 @@
#TOC> #TOC>
#TOC> Section Title Line #TOC> Section Title Line
#TOC> -------------------------------------------------------------------------- #TOC> --------------------------------------------------------------------------
#TOC> 1 Preparations 56 #TOC> 1 Preparations 62
#TOC> 2 Loading a GEO Dataset 82 #TOC> 2 Loading a GEO Dataset 89
#TOC> 3 Column wise analysis - time points 152 #TOC> 2.1 Task - understanding the data 155
#TOC> 3.1 Task - Comparison of experiments 158 #TOC> 3 Column wise analysis - time points 164
#TOC> 3.2 Grouped Samples 205 #TOC> 3.1 Task - Comparison of experiments 193
#TOC> 4 Row-wise Analysis: Expression Profiles 240 #TOC> 3.2 Grouped Samples 226
#TOC> 4.1 Task - Read a table of features 275 #TOC> 4 Row-wise Analysis: Expression Profiles 261
#TOC> 4.2 Selected Expression profiles 323 #TOC> 4.1 Task - Read a table of features 296
#TOC> 5 Differential Expression 364 #TOC> 4.2 Selected Expression profiles 349
#TOC> 5.1 Final task: Gene descriptions 504 #TOC> 5 Differential Expression 392
#TOC> 6 Improving on Discovery by Differential Expression 510 #TOC> 5.1 Final task: Gene descriptions 532
#TOC> 7 Annotation data 594 #TOC> 6 Improving on Discovery by Differential Expression 538
#TOC> 7 Annotation data 633
#TOC> #TOC>
#TOC> ========================================================================== #TOC> ==========================================================================
@ -165,7 +152,7 @@ Biobase::sampleNames(GSE3635)[1:10] # Columns. What are these columns?
# Access data # Access data
Biobase::exprs(tmp) # exprs() gives us the actual expression values. 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> What are the data values:
#TASK> ... in each cell? #TASK> ... in each cell?