[BioC] Problem running summarizeOverlaps()

[Jessica Perry Hekman]

On 05/20/2014 04:25 PM, Martin Morgan wrote:

> If you do decide to update your R, summarizeOverlaps has moved to
> GenomicAlignments.

So I figured if I was going to be having this much trouble I might as 
well be on the latest R in case that helped. So I upgraded to 3.1.0 and 
the latest Bioconductor. I modified my script a bit as below. And now I 
have a new error message, at that same line that we had just gotten 
working in the old version (augh).


source("http://bioconductor.org/biocLite.R")
biocLite(c("GenomicFeatures", "GenomicAlignments", "pathview", "gage", 
"gageData", "Rsamtools", "leeBamViews"))

# Build data object: Dog
txdb.canFam3 <- 
GenomicFeatures::makeTranscriptDbFromUCSC("canFam3","refGene")
exByGn <- GenomicFeatures::exonsBy(txdb.canFam3, "gene")

# Read counts
library(Rsamtools)
fls <- list.files("../../bam/", pattern="-fox-readgroups.bam$", 
full.names=T)

library(leeBamViews)
bamfls <- BamFileList(fls, yieldSize=100000)

flag <- scanBamFlag(isNotPrimaryRead=FALSE, isProperPair=TRUE)
param <- ScanBamParam(flag=flag)

# Count only reads which match exactly once ("Union")
options(mc.cores=8)
gnCnt <- GenomicAlignments::summarizeOverlaps(exByGn, bamfls, mode="Union",
          ignore.strand=TRUE, single.end=TRUE, param=param)

OUTPUT:

Error in array(x, c(length(x), 1L), if (!is.null(names(x)))
list(names(x),  :
   'data' must be of a vector type, was 'NULL'


And, because all my packages have changed now:

 > sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
  [1] leeBamViews_1.0.0    BSgenome_1.32.0      Biobase_2.24.0
  [4] Rsamtools_1.16.0     Biostrings_2.32.0    XVector_0.4.0
  [7] GenomicRanges_1.16.3 GenomeInfoDb_1.0.2   IRanges_1.22.6
[10] BiocGenerics_0.10.0  BiocInstaller_1.14.2

loaded via a namespace (and not attached):
  [1] AnnotationDbi_1.26.0    BatchJobs_1.2           BBmisc_1.6 

  [4] BiocParallel_0.6.0      biomaRt_2.20.0          bitops_1.0-6 

  [7] brew_1.0-6              codetools_0.2-8         DBI_0.2-7 

[10] digest_0.6.4            fail_1.2                foreach_1.4.2
[13] GenomicAlignments_1.0.1 GenomicFeatures_1.16.0  iterators_1.0.7
[16] plyr_1.8.1              Rcpp_0.11.1             RCurl_1.95-4.1
[19] RSQLite_0.11.4          rtracklayer_1.24.1      sendmailR_1.1-2
[22] stats4_3.1.0            stringr_0.6.2           tools_3.1.0
[25] XML_3.98-1.1            zlibbioc_1.10.0
 >

I feel badly continuing to ask for help, but these error messages are 
beyond me. In this case, my best guess was that the message is saying 
that I got the signature of the method wrong -- but when I tried 
changing my arguments, I got a message saying "no method matches that 
signature," so I conclude that that's not the problem.

Thanks,
Jessica