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add jsonlite:: to fromjJSON() in code sample

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hyginn 2020-10-02 18:27:59 +10:00
parent d38092f08a
commit e974fbdb10
1 changed files with 17 additions and 14 deletions
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31
BIN-ALI-Optimal_sequence_alignment.R
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@ -3,12 +3,13 @@
# Purpose: A Bioinformatics Course: # Purpose: A Bioinformatics Course:
# R code accompanying the BIN-ALI-Optimal_sequence_alignment unit. # R code accompanying the BIN-ALI-Optimal_sequence_alignment unit.
# #
# Version: 1.7 # Version: 1.7.1
# #
# Date: 2017-09 - 2020-09 # Date: 2017-09 - 2020-10
# Author: Boris Steipe (boris.steipe@utoronto.ca) # Author: Boris Steipe (boris.steipe@utoronto.ca)
# #
# Versions: # Versions:
# 1.7.1 add jsonlite:: to fromjJSON() in code sample
# 1.7 2020 updates # 1.7 2020 updates
# 1.6 Maintenance # 1.6 Maintenance
# 1.5 Change from require() to requireNamespace(), # 1.5 Change from require() to requireNamespace(),
@ -39,16 +40,16 @@
#TOC> #TOC>
#TOC> Section Title Line #TOC> Section Title Line
#TOC> -------------------------------------------------------------------------- #TOC> --------------------------------------------------------------------------
#TOC> 1 Prepare 56 #TOC> 1 Prepare 57
#TOC> 2 Biostrings Pairwise Alignment 73 #TOC> 2 Biostrings Pairwise Alignment 74
#TOC> 2.1 Optimal global alignment 91 #TOC> 2.1 Optimal global alignment 92
#TOC> 2.2 Optimal local alignment 154 #TOC> 2.2 Optimal local alignment 155
#TOC> 3 APSES Domain annotation by alignment 178 #TOC> 3 APSES Domain annotation by alignment 179
#TOC> 4 Update your database script 259 #TOC> 4 Update your database script 260
#TOC> 4.1 Preparing an annotation file ... 265 #TOC> 4.1 Preparing an annotation file ... 266
#TOC> 4.1.1 If you HAVE NOT done the BIN-FUNC-Annotation unit 267 #TOC> 4.1.1 If you HAVE NOT done the BIN-FUNC-Annotation unit 268
#TOC> 4.1.2 If you HAVE done the BIN-FUNC-Annotation unit 310 #TOC> 4.1.2 If you HAVE done the BIN-FUNC-Annotation unit 313
#TOC> 4.2 Execute and Validate 334 #TOC> 4.2 Execute and Validate 337
#TOC> #TOC>
#TOC> ========================================================================== #TOC> ==========================================================================
@ -300,8 +301,10 @@ aliApses@subject@range@start + aliApses@subject@range@width - 1
# annotation when you recreate the database. Open the script in the # annotation when you recreate the database. Open the script in the
# RStudio editor, and add the following command at the end: # RStudio editor, and add the following command at the end:
# #
# myDB <- dbAddAnnotation(myDB, fromJSON("<MYSPE>-Annotations.json")) # myDB <- dbAddAnnotation(myDB,
# # jsonlite::fromJSON("<MYSPE>-Annotations.json"))
# ^^^^^^^
# edit this!
# - save and close the file. # - save and close the file.
# #
# Then SKIP the next section. # Then SKIP the next section.