ydeng/bch441-work-abc-units
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

add jsonlite:: to fromjJSON() in code sample

Browse Source
This commit is contained in:
hyginn 2020-10-02 18:27:59 +10:00
parent d38092f08a
commit e974fbdb10
1 changed files with 17 additions and 14 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

31
BIN-ALI-Optimal_sequence_alignment.R
View File

@ -3,12 +3,13 @@
# Purpose: A Bioinformatics Course:
# 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)
#
# Versions:
# 1.7.1 add jsonlite:: to fromjJSON() in code sample
# 1.7 2020 updates
# 1.6 Maintenance
# 1.5 Change from require() to requireNamespace(),
@ -39,16 +40,16 @@
#TOC>
#TOC> Section Title Line
#TOC> --------------------------------------------------------------------------
#TOC> 1 Prepare 56
#TOC> 2 Biostrings Pairwise Alignment 73
#TOC> 2.1 Optimal global alignment 91
#TOC> 2.2 Optimal local alignment 154
#TOC> 3 APSES Domain annotation by alignment 178
#TOC> 4 Update your database script 259
#TOC> 4.1 Preparing an annotation file ... 265
#TOC> 4.1.1 If you HAVE NOT done the BIN-FUNC-Annotation unit 267
#TOC> 4.1.2 If you HAVE done the BIN-FUNC-Annotation unit 310
#TOC> 4.2 Execute and Validate 334
#TOC> 1 Prepare 57
#TOC> 2 Biostrings Pairwise Alignment 74
#TOC> 2.1 Optimal global alignment 92
#TOC> 2.2 Optimal local alignment 155
#TOC> 3 APSES Domain annotation by alignment 179
#TOC> 4 Update your database script 260
#TOC> 4.1 Preparing an annotation file ... 266
#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 313
#TOC> 4.2 Execute and Validate 337
#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
# 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.
#
# Then SKIP the next section.