ydeng/bch441-work-abc-units
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specify package when attaching BLOSUM62 - don't assume Biostrings has been loaded.

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hyginn 2020-10-02 20:59:29 +10:00
parent 152d01273f
commit efb52f636d
2 changed files with 17 additions and 16 deletions
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29
BIN-ALI-MSA.R
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@ -38,16 +38,16 @@
#TOC> 2.1 Preparing Sequences 108 #TOC> 2.1 Preparing Sequences 108
#TOC> 2.2 Compute the MSA 133 #TOC> 2.2 Compute the MSA 133
#TOC> 3 Analyzing an MSA 154 #TOC> 3 Analyzing an MSA 154
#TOC> 4 Comparing MSAs 225 #TOC> 4 Comparing MSAs 226
#TOC> 4.1 Importing an alignment to msa 234 #TOC> 4.1 Importing an alignment to msa 235
#TOC> 4.1.1 importing an .aln file 243 #TOC> 4.1.1 importing an .aln file 244
#TOC> 4.1.2 Creating an MsaAAMultipleAlignment object 274 #TOC> 4.1.2 Creating an MsaAAMultipleAlignment object 275
#TOC> 4.2 More alignments 325 #TOC> 4.2 More alignments 326
#TOC> 4.3 Computing comparison metrics 337 #TOC> 4.3 Computing comparison metrics 338
#TOC> 5 Profile-Profile alignments 475 #TOC> 5 Profile-Profile alignments 476
#TOC> 6 Sequence Logos 548 #TOC> 6 Sequence Logos 549
#TOC> 6.1 Subsetting an alignment by motif 557 #TOC> 6.1 Subsetting an alignment by motif 558
#TOC> 6.2 Plot a Sequence Logo 606 #TOC> 6.2 Plot a Sequence Logo 607
#TOC> #TOC>
#TOC> ========================================================================== #TOC> ==========================================================================
@ -56,10 +56,10 @@
# You need to reload you protein database, including changes that might # You need to reload you protein database, including changes that might
# have been made to the reference files. If you have worked with the # have been made to the reference files. If you have worked with the
# prerequiste units, you should have a script named "makeProteinDB.R" # prerequisite units, you should have a script named "./myScripts/makeProteinDB.R"
# that will create the myDB object with a protein and feature database. # that will create the myDB object with a protein and feature database.
# Ask for advice if not. # Ask for advice if not.
source("makeProteinDB.R") source("./myScripts/makeProteinDB.R")
if (! requireNamespace("BiocManager", quietly=TRUE)) { if (! requireNamespace("BiocManager", quietly=TRUE)) {
@ -168,7 +168,8 @@ msa::print(msaM, show=c("alignment", "complete"), showConsensus=FALSE)
# in a column from n sequences; # in a column from n sequences;
# - therefore the column score is 8 * (11^2 - 11) / 2 == 440 # - therefore the column score is 8 * (11^2 - 11) / 2 == 440
data("BLOSUM62") # fetch the BLOSUM62 package from the Biostrings package # attach the BLOSUM62 package from the Biostrings package
data(BLOSUM62, package = "Biostrings")
msaMScores <- msa::msaConservationScore(msaM, substitutionMatrix = BLOSUM62) msaMScores <- msa::msaConservationScore(msaM, substitutionMatrix = BLOSUM62)
plot(msaMScores, type = "l", col = "#205C5E", xlab = "Alignment Position") plot(msaMScores, type = "l", col = "#205C5E", xlab = "Alignment Position")
@ -423,7 +424,7 @@ legend("topright",
cex = 0.7, cex = 0.7,
bty = "n") bty = "n")
# The desnity plots confirm in more detail that CLUSTAL W misses some of the # The density plots confirm in more detail that CLUSTAL W misses some of the
# higher-scoring possibilities, that wherever CLUSTAL O is bad, it is quite bad, # higher-scoring possibilities, that wherever CLUSTAL O is bad, it is quite bad,
# that T-COFFEE has fewer poorly scoring columns but misses some of the better # that T-COFFEE has fewer poorly scoring columns but misses some of the better
# scoring possibilities, and that MUSCLE appears to do best overall. # scoring possibilities, and that MUSCLE appears to do best overall.

4
BIN-ALI-Similarity.R
View File

@ -203,8 +203,8 @@ if (! requireNamespace("Biostrings", quietly=TRUE)) {
# browseVignettes("Biostrings") # available vignettes # browseVignettes("Biostrings") # available vignettes
# data(package = "Biostrings") # available datasets # data(package = "Biostrings") # available datasets
# Let's load the BLOSUM62 mutation data matrix from the package # Let's attach the BLOSUM62 mutation data matrix from the package
data(BLOSUM62) data(BLOSUM62, package = "Biostrings")
# ... and see what it contains. (You've seen this matrix before.) # ... and see what it contains. (You've seen this matrix before.)
BLOSUM62 BLOSUM62