diff --git a/BIN-Storing_data.R b/BIN-Storing_data.R index 68f955a..2ac9452 100644 --- a/BIN-Storing_data.R +++ b/BIN-Storing_data.R @@ -3,11 +3,12 @@ # Purpose: A Bioinformatics Course: # R code accompanying the BIN-Storing_data unit # -# Version: 1.3.1 +# Version: 1.3.2 # -# Date: 2017-10 - 2020-09 +# Date: 2017-10 - 2021-09 # Author: Boris Steipe (boris.steipe@utoronto.ca) # +# V 1.3.2 2021 minimal maintenance # V 1.3.1 add overlooked jsonlite:: prefix to fromJson() # V 1.3 Made file locations more consistent. All student-edited files # go into the myScripts directory @@ -32,30 +33,30 @@ #TOC> ========================================================================== -#TOC> +#TOC> #TOC> Section Title Line #TOC> ----------------------------------------------------------------------- -#TOC> 1 A Relational Datamodel in R: review 62 -#TOC> 1.1 Building a sample database structure 102 -#TOC> 1.1.1 completing the database 208 -#TOC> 1.2 Querying the database 241 -#TOC> 1.3 Task: submit for credit (part 1/2) 272 -#TOC> 2 Implementing the protein datamodel 294 -#TOC> 2.1 JSON formatted source data 320 -#TOC> 2.2 "Sanitizing" sequence data 361 -#TOC> 2.3 Create a protein table for our data model 383 -#TOC> 2.3.1 Initialize the database 385 -#TOC> 2.3.2 Add data 397 -#TOC> 2.4 Complete the database 417 -#TOC> 2.4.1 Examples of navigating the database 444 -#TOC> 2.5 Updating the database 476 -#TOC> 3 Add your own data 488 -#TOC> 3.1 Find a protein 496 -#TOC> 3.2 Put the information into JSON files 526 -#TOC> 3.3 Create an R script to create your own database 568 -#TOC> 3.3.1 Check and validate 596 -#TOC> 3.4 Task: submit for credit (part 2/2) 641 -#TOC> +#TOC> 1 A Relational Datamodel in R: review 63 +#TOC> 1.1 Building a sample database structure 103 +#TOC> 1.1.1 completing the database 209 +#TOC> 1.2 Querying the database 242 +#TOC> 1.3 Task: submit for credit (part 1/2) 273 +#TOC> 2 Implementing the protein datamodel 297 +#TOC> 2.1 JSON formatted source data 323 +#TOC> 2.2 "Sanitizing" sequence data 364 +#TOC> 2.3 Create a protein table for our data model 386 +#TOC> 2.3.1 Initialize the database 388 +#TOC> 2.3.2 Add data 400 +#TOC> 2.4 Complete the database 420 +#TOC> 2.4.1 Examples of navigating the database 447 +#TOC> 2.5 Updating the database 479 +#TOC> 3 Add your own data 491 +#TOC> 3.1 Find a protein 499 +#TOC> 3.2 Put the information into JSON files 530 +#TOC> 3.3 Create an R script to create your own database 572 +#TOC> 3.3.1 Check and validate 600 +#TOC> 3.4 Task: submit for credit (part 2/2) 645 +#TOC> #TOC> ========================================================================== @@ -205,7 +206,7 @@ str(philDB) # go back, re-read, play with it, and ask for help. These are the foundations. -# === 1.1.1 completing the database +# === 1.1.1 completing the database # Next I'll add one more person, and create the other two tables: @@ -384,7 +385,7 @@ dbSanitizeSequence(x) # == 2.3 Create a protein table for our data model ========================= -# === 2.3.1 Initialize the database +# === 2.3.1 Initialize the database # The function dbInit contains all the code to return a list of empty @@ -396,7 +397,7 @@ myDB <- dbInit() str(myDB) -# === 2.3.2 Add data +# === 2.3.2 Add data # fromJSON() returns a dataframe that we can readily process to add data @@ -443,7 +444,7 @@ source("./scripts/ABC-createRefDB.R") str(myDB) -# === 2.4.1 Examples of navigating the database +# === 2.4.1 Examples of navigating the database # You can look at the contents of the tables in the usual way we access @@ -596,7 +597,7 @@ if (file.exists(sprintf("./myScripts/%staxonomy.json", biCode(MYSPE)))) { # "break" them with a code experiment. But always have a script with # which you can create what you need. -# === 3.3.1 Check and validate +# === 3.3.1 Check and validate # Is your protein named according to the pattern "MBP1_MYSPE"? It should be.