RnBeads: Error in as.list.default(data.source) : no method for coercing this S4 class to a vector
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Entering edit mode
schasse • 0
@schasse-7152
Last seen 6.1 years ago
United States

Previously I have successfully analyzed this data set using RnBeads.

I have been asked to return to my dataset and remove two subjects'  data from the analysis. I have followed the directions closely to affect this modification and resubmitted the job. But it repeatedly failed (see below). 

So, I have reinstalled the latest R package (3.2.2) via Bioconductor, and reinstalled RnBeads but I get the same error messages. I have run out of ideas.

Below is the code and returns:

> setwd("E:/NIDAMethylData/NIDA06")
> data.dir<-"E:/NIDAMethylData/NIDA06"
> idat.dir <- file.path(data.dir, "")
> sample.annotation <- file.path(data.dir, "NIDA_06samplesheet.csv")
> data.source <- c(idat.dir, sample.annotation)
> analysis.dir <- "E:/NIDAMethylData/NIDA06/20150904test01"
> report.dir <- file.path(analysis.dir, "reports")
> result <- rnb.run.import(data.source=data.source, data.type="infinium.idat.dir", dir.reports=report.dir)
2015-09-04 09:26:31     0.3  STATUS STARTED Loading Data
2015-09-04 09:26:31     0.3    INFO     Number of cores: 1
2015-09-04 09:26:32     0.3    INFO     Loading data of type "infinium.idat.dir"
2015-09-04 09:26:32     0.3  STATUS     STARTED Loading Data from IDAT Files
2015-09-04 09:26:32     0.3    INFO         Added column barcode to the provided sample annotation table
2015-09-04 09:28:56     0.5  STATUS     COMPLETED Loading Data from IDAT Files
2015-09-04 09:29:36     0.4  STATUS     Loaded data from E:/NIDAMethylData/NIDA06
2015-09-04 09:29:43     1.3  STATUS     Added data loading section to the report
2015-09-04 09:29:45     1.1  STATUS     Loaded 96 samples and 485577 sites
2015-09-04 09:29:45     1.1    INFO     Output object is of type RnBeadRawSet
2015-09-04 09:29:49     1.5  STATUS COMPLETED Loading Data

> rnb.set <- result$rnb.set
> rnb.set2 <- remove.samples(rnb.set, samples(rnb.set)[c(24, 36)])
> setdiff(samples(rnb.set), samples(rnb.set2))
[1] "95" "96"
> rnb.options(filtering.sex.chromosomes.removal=TRUE, identifiers.column="Sample_Name")
> rnb.run.analysis(dir.reports=report.dir, sample.sheet=sample.annotation, rnb.set2)
2015-09-04 09:31:26     1.1  STATUS STARTED RnBeads Pipeline
2015-09-04 09:31:27     1.1    INFO     Initialized report index and saved to index.html
2015-09-04 09:31:27     1.1  STATUS     STARTED Loading Data
2015-09-04 09:31:27     1.1    INFO         Number of cores: 1
2015-09-04 09:31:27     1.1    INFO         Loading data of type "idat.dir"
Error in as.list.default(data.source) : 
  no method for coercing this S4 class to a vector

rnbeads error as.vector(data) s4vectors s4 • 1.1k views
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Entering edit mode
schasse • 0
@schasse-7152
Last seen 6.1 years ago
United States

So much for the elegant solution.

 

I have solved this by removing the subjects' from the Sample Annotation files, then deleting the corresponding .idat data files from the data source folders and launching the jobs as previously. R seems to be happily running now, but I get no points for a brute force solution.

 

-S-

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