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hyginn 2020-11-03 21:22:08 +10:00
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commit 7bbd19078f
1 changed files with 19 additions and 11 deletions
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BIN-Storing_data.R
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@ -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 <pre> ... </pre> tags.
# in <pre> ... </pre> 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 <pre> ... </pre>
# tags.