Loading ERRBS data in RnBeads

[neur...@gmail.com]

I am trying to run an analysis with ERRBS data with the 'bismarkCytosine' data format.

First, I find I have set rnb.options(import.bed.style = "bismarkCytosine") before running the dj GUI; as simply choosing 'bismarkcytosine' in the import options dropdown menu does not change the R object accordingly.

After figuring this out, I clicked run and it started the analysis, only to get the following error during loading:


Warning: Error in rnb.section.import: invalid value for object; expected MethyLumiSet or RnBSet
81: stop
80: rnb.section.import
79: rnb.step.import
78: rnb.run.import
77: rnb.run.analysis
73: observeEventHandler [C:\Users\neulite\Documents\R\win-library\3.5\RnBeads\extdata\RnBeadsDJ/app.R#2307]
2: shiny::runApp
1: rnb.run.dj

Any ideas?

Here is the full sequence of events:

2018-10-14 15:05:06 1.0 STATUS STARTED RnBeads Pipeline
2018-10-14 15:05:06 1.0 INFO Analysis Title: RnBeads Analysis
2018-10-14 15:05:06 1.0 INFO Initialized report index and saved to index.html
2018-10-14 15:05:06 1.0 STATUS STARTED Loading Data
2018-10-14 15:05:06 1.0 INFO Number of cores: 1
2018-10-14 15:05:06 1.0 INFO Loading data of type "bed.dir"
2018-10-14 15:05:06 1.0 STATUS STARTED Performing loading test
2018-10-14 15:05:06 1.0 INFO The first 10000 rows will be read from each data file
2018-10-14 15:05:06 1.0 INFO No column with file names specified: will try to find one
2018-10-14 15:05:06 1.0 STATUS STARTED Loading Data From BED Files
2018-10-14 15:05:06 1.0 STATUS STARTED Automatically parsing the provided sample annotation file
2018-10-14 15:05:06 1.0 STATUS Potential file names found in column 2 of the supplied annotation table
2018-10-14 15:05:06 1.0 STATUS COMPLETED Automatically parsing the provided sample annotation file
2018-10-14 15:05:06 1.0 INFO Reading BED file: C:\Users\neulite\Desktop\BED_bis_cytosine\dataset/methylcall.CpG.ES_27M_8917.bed
2018-10-14 15:05:11 0.8 INFO Reading BED file: C:\Users\neulite\Desktop\BED_bis_cytosine\dataset/methylcall.CpG.ES.27M.1_10.24.17.bed
2018-10-14 15:05:16 0.8 INFO Reading BED file: C:\Users\neulite\Desktop\BED_bis_cytosine\dataset/methylcall.CpG.ES.27M.2_10.24.17.bed
2018-10-14 15:05:21 0.8 INFO Reading BED file: C:\Users\neulite\Desktop\BED_bis_cytosine\dataset/methylcall.CpG.ES.34R.1_10.24.17.bed
2018-10-14 15:05:26 0.8 INFO Reading BED file: C:\Users\neulite\Desktop\BED_bis_cytosine\dataset/methylcall.CpG.EC.34R.2_10.24.17.bed
2018-10-14 15:05:31 0.8 INFO Reading BED file: C:\Users\neulite\Desktop\BED_bis_cytosine\dataset/methylcall.CpG.ES.34R.3_10.24.17.bed
2018-10-14 15:05:36 0.8 INFO Reading BED file: C:\Users\neulite\Desktop\BED_bis_cytosine\dataset/methylcall.CpG.ES.WT_10.24.17.bed
2018-10-14 15:05:41 0.8 INFO Reading BED file: C:\Users\neulite\Desktop\BED_bis_cytosine\dataset/methylcall.CpG.ES_WT_82217.bed
2018-10-14 15:05:46 0.8 INFO Reading BED file: C:\Users\neulite\Desktop\BED_bis_cytosine\dataset/methylcall.CpG.ES_WT_8917.bed
2018-10-14 15:05:51 0.8 STATUS Read 9 BED files
2018-10-14 15:05:51 0.8 STATUS Matched chromosomes and strands to annotation
2018-10-14 15:05:51 0.8 STATUS Checked for the presence of sites and coverage
2018-10-14 15:05:51 0.8 STATUS Initialized meth/covg matrices
opening ff C:/Users/neulite/AppData/Local/Temp/RtmpGCBfGC/ff32c57bc138.ff
2018-10-14 15:05:56 0.8 STATUS Combined a data matrix with 37957 sites and 9 samples
2018-10-14 15:05:56 0.8 STATUS Processed all BED files
2018-10-14 15:06:01 0.8 STATUS STARTED Creating RnBiseqSet object
2018-10-14 15:06:31 2.4 WARNING All sites have been removed, returning NULL
2018-10-14 15:06:31 2.4 STATUS COMPLETED Creating RnBiseqSet object
2018-10-14 15:06:31 2.4 STATUS COMPLETED Loading Data From BED Files
2018-10-14 15:06:31 2.4 STATUS STARTED Checking the loaded object
2018-10-14 15:06:32 2.4 INFO The supplied object is not of class RnBiseqSet. Breaking the check...
2018-10-14 15:06:32 2.4 WARNING The object loaded during the loading test contains invalid information (see details above). Please check the whether the data source arguments as well as the data import options, like table separator, BED style or BED column assignment, are set correctly
2018-10-14 15:06:32 2.4 STATUS COMPLETED Checking the loaded object
2018-10-14 15:06:38 2.4 STATUS COMPLETED Performing loading test
2018-10-14 15:06:38 2.4 INFO No column with file names specified: will try to find one
2018-10-14 15:06:39 2.4 STATUS STARTED Loading Data From BED Files
2018-10-14 15:06:39 2.4 STATUS STARTED Automatically parsing the provided sample annotation file
2018-10-14 15:06:39 2.4 STATUS Potential file names found in column 2 of the supplied annotation table
2018-10-14 15:06:39 2.4 STATUS COMPLETED Automatically parsing the provided sample annotation file
2018-10-14 15:06:39 2.4 INFO Reading BED file: C:\Users\neulite\Desktop\BED_bis_cytosine\dataset/methylcall.CpG.ES_27M_8917.bed
2018-10-14 15:07:17 2.7 INFO Reading BED file: C:\Users\neulite\Desktop\BED_bis_cytosine\dataset/methylcall.CpG.ES.27M.1_10.24.17.bed
2018-10-14 15:07:57 2.7 INFO Reading BED file: C:\Users\neulite\Desktop\BED_bis_cytosine\dataset/methylcall.CpG.ES.27M.2_10.24.17.bed
2018-10-14 15:08:21 2.6 INFO Reading BED file: C:\Users\neulite\Desktop\BED_bis_cytosine\dataset/methylcall.CpG.ES.34R.1_10.24.17.bed
2018-10-14 15:08:57 2.7 INFO Reading BED file: C:\Users\neulite\Desktop\BED_bis_cytosine\dataset/methylcall.CpG.EC.34R.2_10.24.17.bed
2018-10-14 15:09:31 2.7 INFO Reading BED file: C:\Users\neulite\Desktop\BED_bis_cytosine\dataset/methylcall.CpG.ES.34R.3_10.24.17.bed
2018-10-14 15:09:49 2.5 INFO Reading BED file: C:\Users\neulite\Desktop\BED_bis_cytosine\dataset/methylcall.CpG.ES.WT_10.24.17.bed
2018-10-14 15:10:20 2.6 INFO Reading BED file: C:\Users\neulite\Desktop\BED_bis_cytosine\dataset/methylcall.CpG.ES_WT_82217.bed
2018-10-14 15:10:45 2.6 INFO Reading BED file: C:\Users\neulite\Desktop\BED_bis_cytosine\dataset/methylcall.CpG.ES_WT_8917.bed
2018-10-14 15:11:10 2.6 STATUS Read 9 BED files
2018-10-14 15:12:04 4.2 STATUS Matched chromosomes and strands to annotation
2018-10-14 15:12:04 4.2 STATUS Checked for the presence of sites and coverage
2018-10-14 15:12:10 4.5 STATUS Initialized meth/covg matrices
opening ff C:/Users/neulite/AppData/Local/Temp/RtmpGCBfGC/ff32c743d6fe5.ff
2018-10-14 15:12:49 3.1 STATUS Combined a data matrix with 28376194 sites and 9 samples
2018-10-14 15:12:49 3.1 STATUS Processed all BED files
2018-10-14 15:12:56 3.1 STATUS STARTED Creating RnBiseqSet object
2018-10-14 15:12:56 4.3 INFO Removed 386 sites with unknown chromosomes
2018-10-14 15:13:56 3.5 WARNING All sites have been removed, returning NULL
2018-10-14 15:13:56 3.5 STATUS COMPLETED Creating RnBiseqSet object
2018-10-14 15:13:56 3.5 STATUS COMPLETED Loading Data From BED Files
2018-10-14 15:14:03 2.4 STATUS STARTED Checking the loaded object
2018-10-14 15:14:03 2.4 INFO The supplied object is not of class RnBiseqSet. Breaking the check...
2018-10-14 15:14:03 2.4 WARNING The loaded object contains invalid information (see details above). Please check the whether the data source arguments as well as the data import options, like table separator, BED style or BED column assignment, are set correctly
2018-10-14 15:14:10 2.4 STATUS COMPLETED Checking the loaded object
2018-10-14 15:14:10 2.4 STATUS Loaded data from C:\Users\neulite\Desktop\BED_bis_cytosine\dataset
Warning: Error in rnb.section.import: invalid value for object; expected MethyLumiSet or RnBSet
81: stop
80: rnb.section.import
79: rnb.step.import
78: rnb.run.import
77: rnb.run.analysis
73: observeEventHandler [C:\Users\neulite\Documents\R\win-library\3.5\RnBeads\extdata\RnBeadsDJ/app.R#2307]
2: shiny::runApp
1: rnb.run.dj