Hi all. I'm trying to get derfinder working. I have some pretty simple code right now:

library(derfinder)
library(Rsamtools)
b1 <- BamFile("tophat/tophat-juncs-10_130/accepted_hits.bam", index="tophat/tophat-juncs-10_130/accepted_hits.bam.bai")
fullCov <- fullCoverage(bl)

When I run this (R 3.1.1, updated Bioconductor yesterday), I get the error:

Error in loadCoverage(files = files, chr = chrs[idx], cutoff = NULL, bai = bai, : Not all BAM files have a BAM index. If the BAM index files are in a separate directory from the BAM files or are not named as 'bamFile.bam.bai' then consider using the 'bai' argument.

The BAI file does exist and I even specified it in the BamFile() call, so I'm not sure what's going on!

Thanks,

Jessica

Hi Jessica,

`fullCoverage()` and `loadCoverage()` can take as input a character vector or a BamFileList object for the `files` argument, not a BamFile object. Your example however lead me to find a small bug when you input a BamFileList. In the meantime, use the functionality where you provide a character vector.

(Edit: BamFile and BigWigFile objects are now supported in `derfinder` versions 1.0.3 and 1.1.3 for release and devel respectively.)

That is, the equivalent of:

> library('derfinder')
> bam <- system.file('extdata', 'genomeData', 'ERR009101_accepted_hits.bam', package = 'derfinder')
> fullCov <- fullCoverage(bam, chrs = '21')
2014-10-16 16:22:24 fullCoverage: processing chromosome 21
2014-10-16 16:22:24 loadCoverage: finding chromosome lengths
2014-10-16 16:22:24 loadCoverage: loading BAM file /Library/Frameworks/R.framework/Versions/3.1/Resources/library/derfinder/extdata/genomeData/ERR009101_accepted_hits.bam
2014-10-16 16:22:24 loadCoverage: applying the cutoff to the merged data
2014-10-16 16:22:24 filterData: originally there were 48129895 rows, now there are 48129895 rows. Meaning that 0 percent was filtered.
> devtools::session_info()
Session info-----------------------------------------------------------------------------------------------------------------------------------
 setting  value                       
 version  R version 3.1.1 (2014-07-10)
 system   x86_64, darwin10.8.0        
 ui       AQUA                        
 language (EN)                        
 collate  en_US.UTF-8                 
 tz       America/New_York            

Packages---------------------------------------------------------------------------------------------------------------------------------------
 package           * version  date       source        
 acepack             1.3.3.3  2013-05-03 CRAN (R 3.1.0)
 AnnotationDbi       1.28.0   2014-10-14 Bioconductor  
 base64enc           0.1.2    2014-06-26 CRAN (R 3.1.0)
 BatchJobs           1.4      2014-09-24 CRAN (R 3.1.1)
 BBmisc              1.7      2014-06-21 CRAN (R 3.1.0)
 Biobase             2.26.0   2014-10-14 Bioconductor  
 BiocGenerics        0.12.0   2014-10-14 Bioconductor  
 BiocParallel        1.0.0    2014-10-15 Bioconductor  
 biomaRt             2.22.0   2014-10-14 Bioconductor  
 Biostrings          2.34.0   2014-10-14 Bioconductor  
 bitops              1.0.6    2013-08-17 CRAN (R 3.1.0)
 brew                1.0.6    2011-04-13 CRAN (R 3.1.0)
 bumphunter          1.6.0    2014-10-14 Bioconductor  
 checkmate           1.4      2014-09-03 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         * 1.1.2    2014-10-14 Bioconductor  
 derfinderHelper     1.0.1    2014-10-15 Bioconductor  
 devtools            1.6.1    2014-10-07 CRAN (R 3.1.1)
 digest              0.6.4    2013-12-03 CRAN (R 3.1.0)
 doRNG               1.6      2014-03-07 CRAN (R 3.1.1)
 fail                1.2      2013-09-19 CRAN (R 3.1.0)
 foreach             1.4.2    2014-04-11 CRAN (R 3.1.0)
 foreign             0.8.61   2014-03-28 CRAN (R 3.1.0)
 Formula             1.1.2    2014-07-13 CRAN (R 3.1.1)
 GenomeInfoDb        1.2.0    2014-10-14 Bioconductor  
 GenomicAlignments   1.2.0    2014-10-14 Bioconductor  
 GenomicFeatures     1.18.0   2014-10-14 Bioconductor  
 GenomicFiles        1.2.0    2014-10-14 Bioconductor  
 GenomicRanges       1.18.1   2014-10-16 Bioconductor  
 Hmisc               3.14.5   2014-09-12 CRAN (R 3.1.1)
 IRanges             2.0.0    2014-10-14 Bioconductor  
 iterators           1.0.7    2014-04-11 CRAN (R 3.1.0)
 lattice             0.20.29  2014-04-04 CRAN (R 3.1.0)
 latticeExtra        0.6.26   2013-08-15 CRAN (R 3.1.0)
 locfit              1.5.9.1  2013-04-20 CRAN (R 3.1.0)
 Matrix              1.1.4    2014-06-15 CRAN (R 3.1.0)
 matrixStats         0.10.0   2014-06-08 CRAN (R 3.1.0)
 nnet                7.3.8    2014-03-28 CRAN (R 3.1.0)
 pkgmaker            0.22     2014-05-14 CRAN (R 3.1.0)
 qvalue              1.40.0   2014-10-14 Bioconductor  
 R.methodsS3         1.6.1    2014-01-05 CRAN (R 3.1.0)
 RColorBrewer        1.0.5    2011-06-17 CRAN (R 3.1.0)
 RCurl               1.95.4.3 2014-07-29 CRAN (R 3.1.1)
 registry            0.2      2012-01-24 CRAN (R 3.1.0)
 rngtools            1.2.4    2014-03-06 CRAN (R 3.1.0)
 rpart               4.1.8    2014-03-28 CRAN (R 3.1.0)
 Rsamtools           1.18.0   2014-10-14 Bioconductor  
 RSQLite             0.11.4   2013-05-26 CRAN (R 3.1.0)
 rstudioapi          0.1      2014-03-27 CRAN (R 3.1.0)
 rtracklayer         1.26.0   2014-10-14 Bioconductor  
 S4Vectors           0.4.0    2014-10-14 Bioconductor  
 sendmailR           1.2.1    2014-09-21 CRAN (R 3.1.1)
 stringr             0.6.2    2012-12-06 CRAN (R 3.1.0)
 survival            2.37.7   2014-01-22 CRAN (R 3.1.0)
 XML                 3.98.1.1 2013-06-20 CRAN (R 3.1.0)
 xtable              1.7.4    2014-09-12 CRAN (R 3.1.1)
 XVector             0.6.0    2014-10-14 Bioconductor  
 zlibbioc            1.12.0   2014-10-14 Bioconductor  

Cheers,
Leo

Perfect -- I tried a character vector and it worked great. Thanks for your fast answer!

Jessica