I'm trying to get derfinder working with my RNA-seq reads which are aligned to dog (Canis familiaris 3.1) since its update to work with the recent bumphunter update to support non-human data.

I have dog transcripts in a "tx" object which I believe is built appropriately (I've used it successfully in the past).

First:

for (chr in chroms ) {
  currentChrom <- paste("chr", chr, sep="")
  print(currentChrom)
  dir.create(currentChrom)
  results <- analyzeChr(chr = currentChrom, filteredCov[[currentChrom]], models, mc.cores=cores, groupInfo = groups, cutoffFstat = fstat, cutoffType = 'manual', nPermute = perms, seeds = 19731107 + seq_len(perms), lowMemDir = file.path(tempdir(), currentChrom), BPPARAM.custom = MulticoreParam(workers = cores), verbose = TRUE, runAnnotation = TRUE, writeOutput = TRUE, returnOutput = TRUE, subject=tx)
}

This gives the error:

> Error in annotateNearest(regions$regions, subject) :
>  arguments must be both IRanges or GRanges

My tx object is a GRanges. I found that this workaround got me past this problem:

for (chr in chroms ) {
  currentChrom <- paste("chr", chr, sep="")
  print(currentChrom)
  dir.create(currentChrom)
  results <- analyzeChr(chr = currentChrom, filteredCov[[currentChrom]], models, mc.cores=cores, groupInfo = groups, cutoffFstat = fstat, cutoffType = 'manual', nPermute = perms, seeds = 19731107 + seq_len(perms), lowMemDir = file.path(tempdir(), currentChrom), BPPARAM.custom = MulticoreParam(workers = cores), verbose = TRUE, runAnnotation = FALSE, writeOutput = TRUE, returnOutput = TRUE, subject=tx)
  annotation <- annotateNearest(results$regions$regions, tx)
  save(annotation, file = file.path(currentChrom, 'annotation.Rdata'))
}

Now analyzeChr() completes. However:

mergeResults(chrs=paste("chr", chroms, sep=""), prefix=derResults,
   genomicState = genomicState$fullGenome,
   optionsStats = results$optionsStats)

2014-12-21 11:11:25 mergeResults: Saving options used
2014-12-21 11:11:25 Loading chromosome chr1
...
2014-12-21 11:11:32 Loading chromosome chr38
2014-12-21 11:11:32 Loading chromosome chrX
Error in `$<-.data.frame`(`*tmp*`, "name", value = character(0)) :
  replacement has 0 rows, data has 204530
Calls: mergeResults -> $<- -> $<-.data.frame
Execution halted

I'm not sure how to approach this one. Help?

> devtools::session_info()
Session info-------------------------------------------------------------------
 setting  value                       
 version  R version 3.1.1 (2014-07-10)
 system   x86_64, linux-gnu           
 ui       X11                         
 language (EN)                        
 collate  en_US.UTF-8                 
 tz       America/Chicago             

Packages-----------------------------------------------------------------------
 package           * version  date       source        
 acepack             1.3.3.3  2013-05-03 CRAN (R 3.1.1)
 AnnotationDbi       1.28.1   2014-10-30 Bioconductor  
 base64enc           0.1.2    2014-06-26 CRAN (R 3.1.1)
 BatchJobs           1.5      2014-10-30 CRAN (R 3.1.1)
 BBmisc              1.8      2014-10-30 CRAN (R 3.1.1)
 Biobase             2.26.0   2014-10-15 Bioconductor  
 BiocGenerics        0.12.1   2014-11-19 Bioconductor  
 BiocParallel        1.0.0    2014-11-11 Bioconductor  
 biomaRt             2.22.0   2014-10-15 Bioconductor  
 Biostrings          2.34.1   2014-12-15 Bioconductor  
 bitops              1.0.6    2013-08-17 CRAN (R 3.0.2)
 brew                1.0.6    2011-04-13 CRAN (R 3.1.1)
 bumphunter          1.6.0    2014-12-17 Bioconductor  
 checkmate           1.5.1    2014-12-14 CRAN (R 3.1.1)
 cluster             1.15.3   2014-09-04 CRAN (R 3.1.1)
 codetools           0.2.9    2014-08-21 CRAN (R 3.1.1)
 DBI                 0.3.1    2014-09-24 CRAN (R 3.1.1)
 derfinder         * 1.0.10   2014-12-21 Bioconductor  
 derfinderHelper     1.0.4    2014-11-10 Bioconductor  
 devtools            1.6.1    2014-10-07 CRAN (R 3.1.1)
 digest              0.6.7    2014-12-20 CRAN (R 3.1.1)
 doRNG               1.6      2014-03-07 CRAN (R 3.1.1)
 fail                1.2      2013-09-19 CRAN (R 3.1.1)
 foreach             1.4.2    2014-04-11 CRAN (R 3.1.1)
 foreign             0.8.61   2014-03-28 CRAN (R 3.1.1)
 Formula             1.1.2    2014-07-13 CRAN (R 3.1.1)
 GenomeInfoDb        1.2.3    2014-11-17 Bioconductor  
 GenomicAlignments   1.2.1    2014-11-10 Bioconductor  
 GenomicFeatures     1.18.3   2014-12-17 Bioconductor  
 GenomicFiles        1.2.0    2014-10-15 Bioconductor  
 GenomicRanges       1.18.3   2014-11-19 Bioconductor  
 Hmisc               3.14.6   2014-11-22 CRAN (R 3.1.1)
 IRanges             2.0.1    2014-12-15 Bioconductor  
 iterators           1.0.7    2014-04-11 CRAN (R 3.1.1)
 lattice             0.20.29  2014-04-04 CRAN (R 3.1.1)
 latticeExtra        0.6.26   2013-08-15 CRAN (R 3.1.1)
 locfit              1.5.9.1  2013-04-20 CRAN (R 3.0.2)
 Matrix              1.1.4    2014-06-15 CRAN (R 3.1.1)
 matrixStats         0.12.2   2014-12-07 CRAN (R 3.1.1)
 nnet                7.3.8    2014-03-28 CRAN (R 3.1.1)
 pkgmaker            0.22     2014-05-14 CRAN (R 3.1.1)
 qvalue              1.40.0   2014-10-15 Bioconductor  
 R.methodsS3         1.6.1    2014-01-05 CRAN (R 3.1.1)
 RColorBrewer        1.1.2    2014-12-07 CRAN (R 3.1.1)
 RCurl               1.95.4.5 2014-12-06 CRAN (R 3.1.1)
 registry            0.2      2012-01-24 CRAN (R 3.1.1)
 rngtools            1.2.4    2014-03-06 CRAN (R 3.1.1)
 rpart               4.1.8    2014-03-28 CRAN (R 3.1.1)
 Rsamtools           1.18.2   2014-11-11 Bioconductor  
 RSQLite             1.0.0    2014-10-25 CRAN (R 3.1.1)
 rstudioapi          0.1      2014-03-27 CRAN (R 3.1.1)
 rtracklayer         1.26.2   2014-11-11 Bioconductor  
 S4Vectors           0.4.0    2014-10-15 Bioconductor  
 sendmailR           1.2.1    2014-09-21 CRAN (R 3.1.1)
 stringr             0.6.2    2012-12-06 CRAN (R 3.0.2)
 survival            2.37.7   2014-01-22 CRAN (R 3.1.1)
 XML                 3.98.1.1 2013-06-20 CRAN (R 3.0.2)
 xtable              1.7.4    2014-09-12 CRAN (R 3.1.1)
 XVector             0.6.0    2014-10-15 Bioconductor  
 zlibbioc            1.12.0   2014-10-15 Bioconductor  

Jessica

As of version 1.1.17 available from BioC-devel, `derfinder` now works well with `bumphunter` version >= 1.7.3 These versions of the packages now allow users to work with non-human annotations. 

A few key things to look at are:

• bumphunter::matchGenes()
• the 'txdb' argument in derfinder::analyzeChr()

An example of how to  use bumphunter::matchGenes() with Canis familiaris is available at https://github.com/lcolladotor/bumphunter/blob/master/tests/testthat/test_annotation.R#L29-L76

Some details: `derfinder` 1.1.17 requires `bumphunter` 1.1.6 which should soon be available from BioC-devel. This `bumphunter` version corrects for a few minor bugs.