Removed 2021 Update warning
This commit is contained in:
hyginn
parent
4b2bab0f12
commit
5e7b683323
@ -5,20 +5,6 @@
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# ==============================================================================
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# ==============================================================================
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# S T O P :
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# =========
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#
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# 2021
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# UPDATE WARNING!
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# ---------------
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#
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# This file has not yet been updated for coursework. You may inspect it, but
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# do NOT use it for actual coursework as long as this warning is here. Parts
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# of the code and data will change, and if you use this outdated code it will
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# break your setup and workflow.
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#
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# ==============================================================================
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#
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# Version: 1.3
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# Version: 1.3
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#
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#
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# Date: 2017-10 - 2020-09
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# Date: 2017-10 - 2020-09
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@ -46,13 +32,13 @@
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#TOC> ==========================================================================
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#TOC> ==========================================================================
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#TOC>
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#TOC>
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#TOC> Section Title Line
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#TOC> Section Title Line
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#TOC> ---------------------------------------------------
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#TOC> ---------------------------------------------------
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#TOC> 1 Defining the APSES domain 43
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#TOC> 1 Defining the APSES domain 45
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#TOC> 2 Executing the BLAST search 73
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#TOC> 2 Executing the BLAST search 75
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#TOC> 3 Analysing results 95
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#TOC> 3 Analysing results 97
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#TOC>
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#TOC>
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#TOC> ==========================================================================
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#TOC> ==========================================================================
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@ -3,20 +3,6 @@
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#
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#
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# ==============================================================================
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# ==============================================================================
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#
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#
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# S T O P :
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# =========
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#
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# 2021
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# UPDATE WARNING!
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# ---------------
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#
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# This file has not yet been updated for coursework. You may inspect it, but
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# do NOT use it for actual coursework as long as this warning is here. Parts
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# of the code and data will change, and if you use this outdated code it will
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# break your setup and workflow.
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#
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# ==============================================================================
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#
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# Purpose: A Bioinformatics Course:
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# Purpose: A Bioinformatics Course:
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# R code accompanying the BIN-ALI-Dotplot unit.
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# R code accompanying the BIN-ALI-Dotplot unit.
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#
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#
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@ -44,12 +30,12 @@
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#TOC> ==========================================================================
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#TOC> ==========================================================================
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#TOC>
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#TOC>
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#TOC> Section Title Line
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#TOC> Section Title Line
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#TOC> --------------------------------------
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#TOC> --------------------------------------
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#TOC> 1 ___Section___ 39
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#TOC> 1 ___Section___ 42
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#TOC> 2 Tasks 187
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#TOC> 2 Tasks 190
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#TOC>
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#TOC>
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#TOC> ==========================================================================
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#TOC> ==========================================================================
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@ -3,21 +3,6 @@
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# Purpose: A Bioinformatics Course:
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# Purpose: A Bioinformatics Course:
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# R code accompanying the BIN-ALI-MSA unit.
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# R code accompanying the BIN-ALI-MSA unit.
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#
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#
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# ==============================================================================
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#
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# S T O P :
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# =========
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#
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# 2021
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# UPDATE WARNING!
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# ---------------
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#
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# This file has not yet been updated for coursework. You may inspect it, but
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# do NOT use it for actual coursework as long as this warning is here. Parts
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# of the code and data will change, and if you use this outdated code it will
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# break your setup and workflow.
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#
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# ==============================================================================
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# Version: 1.3
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# Version: 1.3
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#
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#
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# Date: 2017-10 - 2020-09
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# Date: 2017-10 - 2020-09
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@ -45,7 +30,7 @@
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#TOC> ==========================================================================
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#TOC> ==========================================================================
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#TOC>
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#TOC>
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#TOC> Section Title Line
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#TOC> Section Title Line
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#TOC> ------------------------------------------------------------------
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#TOC> ------------------------------------------------------------------
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#TOC> 1 Preparations 55
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#TOC> 1 Preparations 55
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@ -63,7 +48,7 @@
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#TOC> 6 Sequence Logos 549
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#TOC> 6 Sequence Logos 549
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#TOC> 6.1 Subsetting an alignment by motif 558
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#TOC> 6.1 Subsetting an alignment by motif 558
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#TOC> 6.2 Plot a Sequence Logo 607
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#TOC> 6.2 Plot a Sequence Logo 607
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#TOC>
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#TOC>
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#TOC> ==========================================================================
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#TOC> ==========================================================================
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@ -256,7 +241,7 @@ for (i in seq_along(highScoringRanges$lengths)) {
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# - adjust the sequence names
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# - adjust the sequence names
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# - convert to msaAAMultipleAlignment object
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# - convert to msaAAMultipleAlignment object
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# === 4.1.1 importing an .aln file
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# === 4.1.1 importing an .aln file
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# The seqinr package has a function to read CLUSTAL W formatted .aln files ...
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# The seqinr package has a function to read CLUSTAL W formatted .aln files ...
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if (! requireNamespace("seqinr", quietly=TRUE)) {
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if (! requireNamespace("seqinr", quietly=TRUE)) {
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# R code accompanying the BIN-ALI-Optimal_sequence_alignment unit.
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# R code accompanying the BIN-ALI-Optimal_sequence_alignment unit.
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#
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#
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# ==============================================================================
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# ==============================================================================
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#
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# S T O P :
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# =========
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#
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# 2021
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# UPDATE WARNING!
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# ---------------
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#
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# This file has not yet been updated for coursework. You may inspect it, but
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# do NOT use it for actual coursework as long as this warning is here. Parts
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# of the code and data will change, and if you use this outdated code it will
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# break your setup and workflow.
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#
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# ==============================================================================
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# Version: 1.7.1
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# Version: 1.7.1
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#
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#
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# Date: 2017-09 - 2020-10
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# Date: 2017-09 - 2020-10
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#TOC> ==========================================================================
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#TOC> ==========================================================================
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#TOC>
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#TOC>
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#TOC> Section Title Line
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#TOC> Section Title Line
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#TOC> --------------------------------------------------------------------------
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#TOC> --------------------------------------------------------------------------
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#TOC> 1 Prepare 57
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#TOC> 1 Prepare 58
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#TOC> 2 Biostrings Pairwise Alignment 74
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#TOC> 2 Biostrings Pairwise Alignment 75
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#TOC> 2.1 Optimal global alignment 92
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#TOC> 2.1 Optimal global alignment 93
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#TOC> 2.2 Optimal local alignment 155
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#TOC> 2.2 Optimal local alignment 156
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#TOC> 3 APSES Domain annotation by alignment 179
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#TOC> 3 APSES Domain annotation by alignment 180
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#TOC> 4 Update your database script 260
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#TOC> 4 Update your database script 261
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#TOC> 4.1 Preparing an annotation file ... 266
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#TOC> 4.1 Preparing an annotation file ... 267
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#TOC> 4.1.1 If you HAVE NOT done the BIN-FUNC-Annotation unit 268
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#TOC> 4.1.1 If you HAVE NOT done the BIN-FUNC-Annotation unit 269
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#TOC> 4.1.2 If you HAVE done the BIN-FUNC-Annotation unit 313
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#TOC> 4.1.2 If you HAVE done the BIN-FUNC-Annotation unit 314
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#TOC> 4.2 Execute and Validate 337
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#TOC> 4.2 Execute and Validate 338
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#TOC>
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#TOC>
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#TOC> ==========================================================================
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#TOC> ==========================================================================
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@ -325,7 +311,7 @@ aliApses@subject@range@start + aliApses@subject@range@width - 1
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# Then SKIP the next section.
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# Then SKIP the next section.
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#
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#
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#
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#
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# === 4.1.2 If you HAVE done the BIN-FUNC-Annotation unit
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# === 4.1.2 If you HAVE done the BIN-FUNC-Annotation unit
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#
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#
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#
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# You DO already have a file called "<MYSPE>-Annotations.json" in the
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# You DO already have a file called "<MYSPE>-Annotations.json" in the
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# R code accompanying the BIN-FUNC-Domain_annotation unit.
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# R code accompanying the BIN-FUNC-Domain_annotation unit.
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#
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#
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# ==============================================================================
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# ==============================================================================
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#
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# S T O P :
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# =========
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#
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# 2021
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# UPDATE WARNING!
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# ---------------
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#
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# This file has not yet been updated for coursework. You may inspect it, but
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# do NOT use it for actual coursework as long as this warning is here. Parts
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# of the code and data will change, and if you use this outdated code it will
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# break your setup and workflow.
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#
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# ==============================================================================
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# Version: 1.4
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# Version: 1.4
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#
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#
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# Date: 2017-11 - 2020-10
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# Date: 2017-11 - 2020-10
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#TOC> ==========================================================================
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#TOC> ==========================================================================
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#TOC>
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#TOC>
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#TOC> Section Title Line
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#TOC> Section Title Line
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#TOC> ---------------------------------------------------------------------
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#TOC> ---------------------------------------------------------------------
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#TOC> 1 Update your database script 50
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#TOC> 1 Update your database script 51
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#TOC> 1.1 Preparing an annotation file ... 57
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#TOC> 1.1 Preparing an annotation file ... 58
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#TOC> 1.1.1 BEFORE "BIN-ALI-Optimal_sequence_alignment" 60
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#TOC> 1.1.1 BEFORE "BIN-ALI-Optimal_sequence_alignment" 61
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#TOC> 1.1.2 AFTER "BIN-ALI-Optimal_sequence_alignment" 108
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#TOC> 1.1.2 AFTER "BIN-ALI-Optimal_sequence_alignment" 109
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#TOC> 1.2 Execute and Validate 135
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#TOC> 1.2 Execute and Validate 136
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#TOC> 2 Plot Annotations 160
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#TOC> 2 Plot Annotations 161
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#TOC> 3 SHARING DATA 286
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#TOC> 3 SHARING DATA 287
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#TOC> 3.1 Post MBP1_MYSPE as JSON data 302
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#TOC> 3.1 Post MBP1_MYSPE as JSON data 303
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#TOC> 3.2 Import shared MBP1_MYSPE from the Wiki 325
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#TOC> 3.2 Import shared MBP1_MYSPE from the Wiki 326
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#TOC>
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#TOC>
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#TOC> ==========================================================================
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#TOC> ==========================================================================
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# Then SKIP the next section.
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# Then SKIP the next section.
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#
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#
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#
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#
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# === 1.1.2 AFTER "BIN-ALI-Optimal_sequence_alignment"
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# === 1.1.2 AFTER "BIN-ALI-Optimal_sequence_alignment"
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#
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#
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# IF YOU HAVE ALREADY COMPLETED THE BIN-ALI-OPTIMAL_SEQUENCE_ALIGNMENT UNIT:
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# IF YOU HAVE ALREADY COMPLETED THE BIN-ALI-OPTIMAL_SEQUENCE_ALIGNMENT UNIT:
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#
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#
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#
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#
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# ==============================================================================
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# ==============================================================================
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#
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#
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# S T O P :
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# =========
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#
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# 2021
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# UPDATE WARNING!
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# ---------------
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#
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# This file has not yet been updated for coursework. You may inspect it, but
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# do NOT use it for actual coursework as long as this warning is here. Parts
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# of the code and data will change, and if you use this outdated code it will
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# break your setup and workflow.
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#
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# ==============================================================================
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#
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# Purpose: A Bioinformatics Course:
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# Purpose: A Bioinformatics Course:
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# R code accompanying the FND-STA-Information_theory unit.
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# R code accompanying the FND-STA-Information_theory unit.
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#
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# ==============================================================================
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# ==============================================================================
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#TOC> ==========================================================================
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#TOC>
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#TOC> Section Title Line
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#TOC> --------------------------------------
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#TOC> 1 ___Section___ 39
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#TOC>
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#TOC> ==========================================================================
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# = 1 ___Section___
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# = 1 ___Section___ =======================================================
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# What level of information is "significant"
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# What level of information is "significant"
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RPR-GEO2R.R
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# tocID <- "RPR_GEO2R.R"
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# tocID <- "RPR-GEO2R.R"
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#
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#
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# Purpose: A Bioinformatics Course:
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# Purpose: A Bioinformatics Course:
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# R code accompanying the RPR_GEO2R unit.
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# R code accompanying the RPR_GEO2R unit.
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#
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#
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#
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#
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# ==============================================================================
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# ==============================================================================
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#
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# S T O P :
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# =========
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#
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# 2021
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# UPDATE WARNING!
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# ---------------
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#
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# This file has not yet been updated for coursework. You may inspect it, but
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# do NOT use it for actual coursework as long as this warning is here. Parts
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# of the code and data will change, and if you use this outdated code it will
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# break your setup and workflow.
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#
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# ==============================================================================
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# Version: 1.3
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# Version: 1.3
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#
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# Date: 2017-09 - 2020-09
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# Date: 2017-09 - 2020-09
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#TOC> ==========================================================================
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#TOC> ==========================================================================
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#TOC>
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#TOC>
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#TOC> Section Title Line
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#TOC> Section Title Line
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#TOC> --------------------------------------------------------------------------
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#TOC> --------------------------------------------------------------------------
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#TOC> 1 Preparations 56
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#TOC> 1 Preparations 62
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#TOC> 2 Loading a GEO Dataset 82
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#TOC> 2 Loading a GEO Dataset 89
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#TOC> 3 Column wise analysis - time points 152
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#TOC> 2.1 Task - understanding the data 155
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#TOC> 3.1 Task - Comparison of experiments 158
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#TOC> 3 Column wise analysis - time points 164
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#TOC> 3.2 Grouped Samples 205
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#TOC> 3.1 Task - Comparison of experiments 193
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#TOC> 4 Row-wise Analysis: Expression Profiles 240
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#TOC> 3.2 Grouped Samples 226
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#TOC> 4.1 Task - Read a table of features 275
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#TOC> 4 Row-wise Analysis: Expression Profiles 261
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#TOC> 4.2 Selected Expression profiles 323
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#TOC> 4.1 Task - Read a table of features 296
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#TOC> 5 Differential Expression 364
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#TOC> 4.2 Selected Expression profiles 349
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#TOC> 5.1 Final task: Gene descriptions 504
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#TOC> 5 Differential Expression 392
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#TOC> 6 Improving on Discovery by Differential Expression 510
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#TOC> 5.1 Final task: Gene descriptions 532
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#TOC> 7 Annotation data 594
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#TOC> 6 Improving on Discovery by Differential Expression 538
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#TOC>
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#TOC> 7 Annotation data 633
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#TOC>
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#TOC> ==========================================================================
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#TOC> ==========================================================================
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# Access data
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# Access data
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Biobase::exprs(tmp) # exprs() gives us the actual expression values.
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Biobase::exprs(tmp) # exprs() gives us the actual expression values.
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# == 3.1 Task - understanding the data ==================================
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# == 2.1 Task - understanding the data =====================================
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#TASK> What are the data values:
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#TASK> What are the data values:
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#TASK> ... in each cell?
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#TASK> ... in each cell?
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Reference in New Issue
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