maintenance, update file locations, minor bugs
This commit is contained in:
hyginn
parent
092494d9de
commit
866a1c0e8f
@ -1,20 +1,15 @@
|
||||
# tocID <- "BIN-ALI-MSA.R"
|
||||
#
|
||||
# ---------------------------------------------------------------------------- #
|
||||
# PATIENCE ... #
|
||||
# Do not yet work wih this code. Updates in progress. Thank you. #
|
||||
# boris.steipe@utoronto.ca #
|
||||
# ---------------------------------------------------------------------------- #
|
||||
#
|
||||
# Purpose: A Bioinformatics Course:
|
||||
# R code accompanying the BIN-ALI-MSA unit.
|
||||
#
|
||||
# Version: 1.2
|
||||
# Version: 1.3
|
||||
#
|
||||
# Date: 2017 10 - 2019 01
|
||||
# Date: 2017-10 - 2020-09
|
||||
# Author: Boris Steipe (boris.steipe@utoronto.ca)
|
||||
#
|
||||
# Versions:
|
||||
# 1.3 2020 updates
|
||||
# 1.2 Change from require() to requireNamespace(),
|
||||
# use <package>::<function>() idiom throughout
|
||||
# 1.1 Added fetchMSAmotif()
|
||||
@ -35,25 +30,25 @@
|
||||
|
||||
|
||||
#TOC> ==========================================================================
|
||||
#TOC>
|
||||
#TOC>
|
||||
#TOC> Section Title Line
|
||||
#TOC> ------------------------------------------------------------------
|
||||
#TOC> 1 Preparations 54
|
||||
#TOC> 2 Aligning full length MBP1 proteins 96
|
||||
#TOC> 2.1 Preparing Sequences 107
|
||||
#TOC> 2.2 Compute the MSA 132
|
||||
#TOC> 3 Analyzing an MSA 153
|
||||
#TOC> 4 Comparing MSAs 224
|
||||
#TOC> 4.1 Importing an alignment to msa 233
|
||||
#TOC> 4.1.1 importing an .aln file 242
|
||||
#TOC> 4.1.2 Creating an MsaAAMultipleAlignment object 273
|
||||
#TOC> 4.2 More alignments 324
|
||||
#TOC> 4.3 Computing comparison metrics 336
|
||||
#TOC> 5 Profile-Profile alignments 473
|
||||
#TOC> 6 Sequence Logos 546
|
||||
#TOC> 6.1 Subsetting an alignment by motif 555
|
||||
#TOC> 6.2 Plot a Sequence Logo 604
|
||||
#TOC>
|
||||
#TOC> 1 Preparations 55
|
||||
#TOC> 2 Aligning full length MBP1 proteins 97
|
||||
#TOC> 2.1 Preparing Sequences 108
|
||||
#TOC> 2.2 Compute the MSA 133
|
||||
#TOC> 3 Analyzing an MSA 154
|
||||
#TOC> 4 Comparing MSAs 225
|
||||
#TOC> 4.1 Importing an alignment to msa 234
|
||||
#TOC> 4.1.1 importing an .aln file 243
|
||||
#TOC> 4.1.2 Creating an MsaAAMultipleAlignment object 274
|
||||
#TOC> 4.2 More alignments 325
|
||||
#TOC> 4.3 Computing comparison metrics 337
|
||||
#TOC> 5 Profile-Profile alignments 475
|
||||
#TOC> 6 Sequence Logos 548
|
||||
#TOC> 6.1 Subsetting an alignment by motif 557
|
||||
#TOC> 6.2 Plot a Sequence Logo 606
|
||||
#TOC>
|
||||
#TOC> ==========================================================================
|
||||
|
||||
|
||||
@ -211,9 +206,9 @@ for (i in seq_along(highScoringRanges$lengths)) {
|
||||
# threshold (experiment with that a bit), but once we are satisfied, we can use
|
||||
# the boundaries to print the MSA alignments separately for domains.
|
||||
# Unfortunately the msa package provides no native way to extract blocks of the
|
||||
# alignment for further processing, but your .utilities file loads a function to
|
||||
# write alignment objects and sequence sets to .aln formatted output. Have a
|
||||
# look:
|
||||
# alignment for further processing, but your .utilities.R script contains a
|
||||
# function to write alignment objects and sequence sets to .aln formatted
|
||||
# output. Have a look:
|
||||
|
||||
writeALN
|
||||
|
||||
@ -245,7 +240,7 @@ for (i in seq_along(highScoringRanges$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)) {
|
||||
@ -391,6 +386,7 @@ boxplot(list(CLUSTAL.W = msaWScores,
|
||||
CLUSTAL.O = msaOScores,
|
||||
T.COFFEE = msaTScores,
|
||||
MUSCLE = msaMScores),
|
||||
cex.axis = 0.8,
|
||||
col = c("#7D556488", "#74628F88", "#5E78A188", "#3DAEB288"))
|
||||
|
||||
# CLUSTAL W and CLUSTAL O don't look all that different. T-Coffee tends to have
|
||||
@ -503,7 +499,7 @@ DECIPHER::AlignProfiles(msaW@unmasked, msaM@unmasked)
|
||||
m <- as.character(msaM)
|
||||
w <- as.character(msaW)[names(m)]
|
||||
|
||||
(ppa <- DECIPHER::AlignProfiles(msa::AAStringSet(w), msa::AAStringSet(m)))
|
||||
(ppa <- DECIPHER::AlignProfiles(AAStringSet(w), AAStringSet(m)))
|
||||
|
||||
# Conveniently, AlignProfiles() returns an AAStringSet, so we can use our
|
||||
# writeALN function to show it. Here is an arbitrary block, from somewhere in
|
||||
@ -609,12 +605,12 @@ writeALN(fetchMSAmotif(msaM, wing))
|
||||
|
||||
# == 6.2 Plot a Sequence Logo ==============================================
|
||||
|
||||
# There are now several good options to plot sequence logos in R, these include
|
||||
# dagLogo, DiffLogo, Logolas, and motifStack. For our example we will use
|
||||
# ggseqlogo written by by Omar Waghi, a former UofT BCB student who is now at
|
||||
# the EBI.
|
||||
# The Bioconductor seqLogo:: packager handles only DNA sequences, but there are
|
||||
# now several good options to plot sequence logos in R, these include dagLogo,
|
||||
# DiffLogo, Logolas, and motifStack. For our example we will use ggseqlogo
|
||||
# written by by Omar Waghi, a former UofT BCB student who is now at the EBI.
|
||||
|
||||
if (! requireNamspace("ggseqlogo", quietly=TRUE)) {
|
||||
if (! requireNamespace("ggseqlogo", quietly=TRUE)) {
|
||||
install.packages(("ggseqlogo"))
|
||||
}
|
||||
# Package information:
|
||||
|
||||
Loading…
Reference in New Issue
Block a user