diff --git a/BIN-ALI-BLAST.R b/BIN-ALI-BLAST.R index 4a6cc3f..d7014ac 100644 --- a/BIN-ALI-BLAST.R +++ b/BIN-ALI-BLAST.R @@ -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 Parts -# of the code and data will change, and if you use this outdated code it will -# break your setup and workflow.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> ========================================================================== diff --git a/BIN-ALI-Dotplot.R b/BIN-ALI-Dotplot.R index 56ce80e..e7834ac 100644 --- a/BIN-ALI-Dotplot.R +++ b/BIN-ALI-Dotplot.R @@ -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 Parts -# of the code and data will change, and if you use this outdated code it will -# break your setup and workflow.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> ========================================================================== diff --git a/BIN-ALI-MSA.R b/BIN-ALI-MSA.R index 0d9f7dc..0265d21 100644 --- a/BIN-ALI-MSA.R +++ b/BIN-ALI-MSA.R @@ -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)) { diff --git a/BIN-ALI-Optimal_sequence_alignment.R b/BIN-ALI-Optimal_sequence_alignment.R index 27a26e8..54919f2 100644 --- a/BIN-ALI-Optimal_sequence_alignment.R +++ b/BIN-ALI-Optimal_sequence_alignment.R @@ -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 "-Annotations.json" in the diff --git a/BIN-FUNC-Domain_annotation.R b/BIN-FUNC-Domain_annotation.R index 6f7750d..018b056 100644 --- a/BIN-FUNC-Domain_annotation.R +++ b/BIN-FUNC-Domain_annotation.R @@ -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: # diff --git a/FND-STA-Information_theory.R b/FND-STA-Information_theory.R index 0dd0aa2..a5eb783 100644 --- a/FND-STA-Information_theory.R +++ b/FND-STA-Information_theory.R @@ -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" diff --git a/RPR-GEO2R.R b/RPR-GEO2R.R index 85f9e1c..a4820c2 100644 --- a/RPR-GEO2R.R +++ b/RPR-GEO2R.R @@ -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?