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Entering edit mode
Neel Aluru ▴ 460
@neel-aluru-3760
Last seen 5.6 years ago
United States

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)
> setwd("~/Documents/OneDrive/CpG_RRBS_Brain")
> file=system.file("CpG_zr1121_9.bismark.cov", package="BiSeq")

Processing sample sample1 ...
1:

####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 ...
1:

####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)

locale:
[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,

Neel

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Entering edit mode

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?

Thanks,

Neel

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Entering edit mode
@james-w-macdonald-5106
Last seen 3 hours ago
United States

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

readBismark("CpG_zr1121_9.bismark.cov")

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Entering edit mode

Hi, I know this thread is almost 5 years old but I'm a bit stuck so I'm hoping I'll get a reply.

I am in the same directory as all my files, and I am trying to use readBismark. I wish to enter all my samples at the same time, but whenever I try this, I get an error. This I what I have entered:

setwd("~/Desktop/control_nucleated RBC_data")
rrbs <- readBismark("RRBS_C1_S19_bismark_bt2.bismark.cov", "RRBS_C2_S20_bismark_bt2.bismark.cov", colData = DataFrame(row.names = c("control_1", "control_2"), group = "control"))


The error I get is:

Error in readBismark("RRBS_C1_S19_bismark_bt2.bismark.cov", "RRBS_C2_S20_bismark_bt2.bismark.cov",  :
unused argument ("RRBS_C2_S20_bismark_bt2.bismark.cov")


Do you know what I'm doing wrong?

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Entering edit mode

In your code the readBismark function reads the files as separate arguments. For it to work you need to put the file names into a character vector, like this:

rrbs <- readBismark(files = c("RRBS_C1_S19_bismark_bt2.bismark.cov", "RRBS_C2_S20_bismark_bt2.bismark.cov"), colData = DataFrame(row.names = c("control_1", "control_2"), group = c("control", "control")))


I hope this solves the problem. And sorry for the late reply!