From 7bbd19078f19ad773c84ec9d3fda695782ac8f4a Mon Sep 17 00:00:00 2001 From: hyginn Date: Tue, 3 Nov 2020 21:22:08 +1000 Subject: [PATCH] Clarifications --- BIN-Storing_data.R | 30 +++++++++++++++++++----------- 1 file changed, 19 insertions(+), 11 deletions(-) diff --git a/BIN-Storing_data.R b/BIN-Storing_data.R index b3928f3..68f955a 100644 --- a/BIN-Storing_data.R +++ b/BIN-Storing_data.R @@ -32,7 +32,7 @@ #TOC> ========================================================================== -#TOC> +#TOC> #TOC> Section Title Line #TOC> ----------------------------------------------------------------------- #TOC> 1 A Relational Datamodel in R: review 62 @@ -55,7 +55,7 @@ #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> #TOC> ========================================================================== @@ -205,7 +205,7 @@ 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: @@ -288,7 +288,9 @@ for (ID in pID) { # ... etc. # # Show the output of your code. Make sure the code itself is enclosed -# in 
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tags. +# in 
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tags. DO NOT POST A SCREENSHOT OF YOUR OUTPUT, +# BUT COPY THE EXACT, COMPLETE OUTPUT, PASTE IT INTO YOUR SUBMISSION, +# AND FORMAT IT CORRECTLY. # = 2 Implementing the protein datamodel ================================== @@ -382,7 +384,7 @@ 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 @@ -394,7 +396,7 @@ 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 @@ -441,7 +443,7 @@ 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 @@ -518,7 +520,8 @@ myDB$taxonomy$species[sel] # identities) with the N-terminus of the query - i.e. the Query sequence of # the first ~ 100 amino acids. -# - Follow the link to the protein data page, linked from "Accession". +# - If you are submitting this unit for credit, you will need to paste the +# relevant section of the BLAST results into your submission page (see task). # - Follow the link to the protein data page, linked from "Accession". # - From there, in a separate tab, open the link to the taxonomy database page # for MYSPE which is linked from the "ORGANISM" record. @@ -593,7 +596,7 @@ 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. @@ -641,8 +644,13 @@ myDB$protein$RefSeqID[sel] # == 3.4 Task: submit for credit (part 2/2) ================================ -# - On your submission page, note the E-value of your protein and link -# to its NCBI protein database page. +# - On your submission page, copy/paste the BLAST result headers from the +# "Alignments" tab, to demonstrate that the data justifies your choice of +# protein; you don't need to paste the whole alignment, just the header(s). +# Note the relevant values separately: eValue, coverage, %ID etc. and link +# to your protein's NCBI protein database page. (Note: in case there are +# more than one high-scoring segments included for the SAME protein, you +# need to show the results for all of its high-scoring segments.) # - Copy and paste the contents of your two JSON files on your submission # page on the Student Wiki. Make sure they are enclosed in 
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# tags.