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hyginn 2020-09-26 16:45:29 +10:00
parent 16513dc488
commit 12725799e1
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BIN-PHYLO-Data_preparation.R
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@ -1,20 +1,15 @@
# tocID <- "BIN-PHYLO-Data_preparation.R" # tocID <- "BIN-PHYLO-Data_preparation.R"
# #
# ---------------------------------------------------------------------------- #
# PATIENCE ... #
# Do not yet work wih this code. Updates in progress. Thank you. #
# boris.steipe@utoronto.ca #
# ---------------------------------------------------------------------------- #
#
# Purpose: A Bioinformatics Course: # Purpose: A Bioinformatics Course:
# R code accompanying the BIN-PHYLO-Data_preparation unit. # R code accompanying the BIN-PHYLO-Data_preparation unit.
# #
# Version: 1.1 # Version: 1.2
# #
# Date: 2017 10 - 2019 01 # Date: 2017-10 - 2020-09
# Author: Boris Steipe (boris.steipe@utoronto.ca) # Author: Boris Steipe (boris.steipe@utoronto.ca)
# #
# Versions: # Versions:
# 1.2 2020 Maintenance
# 1.1 Change from require() to requireNamespace(), # 1.1 Change from require() to requireNamespace(),
# use <package>::<function>() idiom throughout, # use <package>::<function>() idiom throughout,
# use Biocmanager:: not biocLite() # use Biocmanager:: not biocLite()
@ -38,11 +33,11 @@
#TOC> #TOC>
#TOC> Section Title Line #TOC> Section Title Line
#TOC> --------------------------------------------------------- #TOC> ---------------------------------------------------------
#TOC> 1 Preparations 44 #TOC> 1 Preparations 45
#TOC> 2 Fetching sequences 76 #TOC> 2 Fetching sequences 77
#TOC> 3 Multiple Sequence Alignment 117 #TOC> 3 Multiple Sequence Alignment 118
#TOC> 4 Reviewing and Editing Alignments 136 #TOC> 4 Reviewing and Editing Alignments 137
#TOC> 4.1 Masking workflow 152 #TOC> 4.1 Masking workflow 153
#TOC> #TOC>
#TOC> ========================================================================== #TOC> ==========================================================================
@ -54,7 +49,7 @@
# been made to the reference files. If you have worked with the prerequiste # been made to the reference files. If you have worked with the prerequiste
# units, you should have a script named "makeProteinDB.R" that will create the # units, you should have a script named "makeProteinDB.R" that will create the
# myDB object with a protein and feature database. Ask for advice if not. # myDB object with a protein and feature database. Ask for advice if not.
source("makeProteinDB.R") source("myScripts/makeProteinDB.R")
# Load packages we need # Load packages we need
@ -172,16 +167,16 @@ for (i in 1:nrow(APSESMsa)) {
} }
# inspect the result # inspect the result
msaMatrix[1:7, 1:14] msaMatrix[1:7, 30:40]
# Now let's make a logical vector with an element for each column that selects # Now let's make a logical vector with an element for each column that selects
# which columns should be masked out. # which columns should be masked out.
# The number of hyphens in a column is easy to count. Consider: # The number of hyphens in a column is easy to count. Consider:
msaMatrix[ , 20] msaMatrix[ , 20] # column 20
msaMatrix[ , 20] == "-" msaMatrix[ , 20] == "-" # TRUE for all gap characters
sum(msaMatrix[ , 20] == "-") sum(msaMatrix[ , 20] == "-") # adds 1 for each TRUE
# Thus filling our logical vector is simple: # Thus filling our logical vector is simple:
@ -192,7 +187,7 @@ colMask <- logical(ncol(msaMatrix))
limit <- round(nrow(APSESMsa) * (2/3)) limit <- round(nrow(APSESMsa) * (2/3))
# iterate over all columns, and write TRUE if there are less-or-equal to "limit" # iterate over all columns, and write TRUE if there are less-or-equal to "limit"
# hyphens, FALSE if there are more - i.e. TRUE columns will be used fr analysis # hyphens, FALSE if there are more - i.e. TRUE columns will be used for analysis
# and FALSE columns will be rejected. # and FALSE columns will be rejected.
for (i in 1:ncol(msaMatrix)) { for (i in 1:ncol(msaMatrix)) {
count <- sum(msaMatrix[ , i] == "-") count <- sum(msaMatrix[ , i] == "-")
@ -230,9 +225,9 @@ writeALN(APSESphyloSet)
# several indels from the KILA_ESCCO outgroup sequence. # several indels from the KILA_ESCCO outgroup sequence.
# We save the aligned, masked domains to a file in multi-FASTA format. # We save the aligned, masked domains to a file in the data/ directory,
writeMFA(APSESphyloSet, myCon = "APSESphyloSet.mfa") # in multi-FASTA format.
writeMFA(APSESphyloSet, myCon = "data/APSESphyloSet.mfa")