Question: Unable to read data using readBismark in BiSeq
gravatar for Neel Aluru
4.0 years ago by
Neel Aluru450
United States
Neel Aluru450 wrote:

I apologize for asking a very naive question. I am using BiSeq for the first time and I am having a hard time reading the data. readBismark command seems to be stalled. Any advice would be highly appreciated.

Here is what I am trying to do.

> library(BiSeq)
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: Formula
> setwd("~/Documents/OneDrive/CpG_RRBS_Brain")
> file=system.file("CpG_zr1121_9.bismark.cov", package="BiSeq")

> readBismark(file, colData = DataFrame(row.names="sample1"))
Processing sample sample1 ...

####It is taking a long time and I am not sure if it is even working. Same thing is happening when I give 8 samples at the same time. Here is the code for that.

> file=system.file("CpG_zr1121_9.bismark.cov", "CpG_zr1121_10.bismark.cov", "CpG_zr1121_11.bismark.cov", "CpG_zr1121_12.bismark.cov", "CpG_zr1121_13.bismark.cov", "CpG_zr1121_14.bismark.cov", "CpG_zr1121_15.bismark.cov", "CpG_zr1121_16.bismark.cov", package="BiSeq")

> readBismark(file, colData = DataFrame(row.names="DMSO1", "DMSO2", "DMSO3", "DMSO4", "PCB1", "PCB2", "PCB3", "PCB4"))

Processing sample DMSO1 ...

####Same thing here...It has been in this state for the past 3-4 hours. Each sample is approximately 100 MB. Any help would be highly appreciated.

Session Info()

> sessionInfo()
R version 3.1.3 (2015-03-09)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.5 (Yosemite)

[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices
[6] utils     datasets  methods   base     

other attached packages:
[1] BiSeq_1.6.0          Formula_1.2-1       
[3] GenomicRanges_1.18.4 GenomeInfoDb_1.2.5  
[5] AnnotationHub_1.6.0  IRanges_2.0.1       
[7] S4Vectors_0.4.0      BiocGenerics_0.12.1

Thank you,


biseq readbismark • 944 views
ADD COMMENTlink modified 4.0 years ago by James W. MacDonald51k • written 4.0 years ago by Neel Aluru450

I noticed that the "system.file" is not working.

> file=system.file("CpG_zr1121_9.bismark.cov", package="BiSeq")

> file


# It is returning an empty vector! Is there something wrong in the command?



ADD REPLYlink written 4.0 years ago by Neel Aluru450
Answer: Unable to read data using readBismark in BiSeq
gravatar for James W. MacDonald
4.0 years ago by
United States
James W. MacDonald51k wrote:

You shouldn't be blindly following vignettes. In other words, for a vignette to work when it needs some real data to process, the usual method is to put the data either in with the package, or in a separate data package. In the former instance, using system.file() will allow the vignette to be processed, because system.file() is a way to find the data that was included as part of the package.

But when you are doing 'real' work with your own data, you should be starting R in the same directory as your data, in which case you don't need to tell R where the files are! The default place for R to look for files is its working directory, so you would just do


Also, when you want to add a comment to your question, you shouldn't use the 'Add Answer' box. Because you are obviously not adding an answer. Instead, use the 'ADD COMMENT" button at the bottom of the post you want to comment on.

ADD COMMENTlink written 4.0 years ago by James W. MacDonald51k
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