I'm currently working with the DNaseR package but am having issues performing the footprinting analysis of the DNase Seq data in the specified .bam file.
I performed the example code from ?DNaseR as a test and everything worked well:
> library('DNaseR')
> bamfile <- "chrY_3Kb_wgEncodeUwDgfTh1Aln.bam"
> f <- system.file("extdata", bamfile, package="DNaseR",mustWork= TRUE)
> dgf <- footprints(bam = f, chrN = "chrY", chrL = 3e6, p = 1e-9, width = c(6,40), N=2e6)
To save space, I have omitted the output of >dgf, but it looked fine.
Next, I tried to load another file using the following lines:
>setwd('~/Documents/Bam Files')
>bamfile <- '~/Documents/Bam Files/mybamfile.bam'
>bam.fp <- footprints(bam = bamfile, chrN = "chrY", chrL = 1.5e7, p=1e-9, width = c(6,50), N = 1e5)
...And I received the following error:
Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append) :
subscript contains NAs or out-of-bounds indices
I can't find much information on NSBS or S4Vectors, the package that contains it. As a result I'm not really sure what this error is referring to or how to fix it.
Here's my sessionInfo, in case that helps.
> sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
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] stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] DNaseR_1.4.0 IRanges_2.0.1 S4Vectors_0.4.0 BiocGenerics_0.12.1
[5] BiocInstaller_1.16.1
loaded via a namespace (and not attached):
[1] Biostrings_2.34.1 bitops_1.0-6 GenomeInfoDb_1.2.4 GenomicRanges_1.18.4
[5] Rsamtools_1.18.3 tools_3.1.2 XVector_0.6.0 zlibbioc_1.12.0
Thanks in advance for any help with this problem!
Martin