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 ...
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
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