Hi All,

I am interested in using the ChIPseqR package for the MNASE data. I am new to using R, and I quite don't understand the error i am receiving. 

My input is paired end BAM file, and I executed the following as per the reference manual.

aln1<- readAligned(path,pattern,type="BAM")

sp <- strandPileup(aln1,chrLen=chr,extend=1,plot=FALSE)

Error: UserArgumentMismatch
  if 'shift' is not 0L, then it must be a vector of integer values
  see ?"AlignedRead-class"

I get the same error while using simpleNucCall  straight. I can only find this shift argument in the "coverage" function, which strandPileup is dependent I guess. 

I appreciate any suggestion or help on this. 

PS: My BAM file contains reads from all chromosomes, so the chr here is named integer vector. 

Thanks,

RT

traceback()
16: stop(cond)
15: .throw(SRError("UserArgumentMismatch", "if '%s' is not 0L, then it must be a vector of integer values\n  see %s", 
        "shift", "?\"AlignedRead-class\""))
14: .throw(SRError("UserArgumentMismatch", "if '%s' is not 0L, then it must be a vector of integer values\n  see %s", 
        "shift", "?\"AlignedRead-class\""))
13: .local(x, shift, width, weight, ...)
12: coverage(fwd, extend = ext1, coords = coords, ...)
11: coverage(fwd, extend = ext1, coords = coords, ...)
10: (function (filter, len, extend, aligned, ...) 
    {
        sfilter1 <- filter & strand(aligned) == "+"
        sfilter2 <- filter & strand(aligned) == "-"
        fwd <- aligned[sfilter1]
        rev <- aligned[sfilter2]
        ext1 <- -width(fwd) + as.integer(extend)
        ext2 <- -width(rev) + as.integer(extend)
        counts <- list(coverage(fwd, extend = ext1, coords = coords, 
            ...)[[1]], coverage(coverage(rev, extend = ext2, coords = coords, 
            ...))[[1]])
        counts <- .fixCounts(counts, len)
        if (!compress) 
            counts <- decompress(counts)
        counts
    })(dots[[1L]][[1L]], dots[[2L]][[1L]], dots[[3L]][[1L]], aligned = <S4 object of class "AlignedRead">, 
        list())
9: .Method(..., FUN = FUN, MoreArgs = MoreArgs, SIMPLIFY = SIMPLIFY, 
       USE.NAMES = USE.NAMES)
8: eval(expr, envir, enclos)
7: eval(.dotsCall, env)
6: eval(.dotsCall, env)
5: standardGeneric("mapply")
4: mapply(function(filter, len, extend, aligned, ...) {
       sfilter1 <- filter & strand(aligned) == "+"
       sfilter2 <- filter & strand(aligned) == "-"
       fwd <- aligned[sfilter1]
       rev <- aligned[sfilter2]
       ext1 <- -width(fwd) + as.integer(extend)
       ext2 <- -width(rev) + as.integer(extend)
       counts <- list(coverage(fwd, extend = ext1, coords = coords, 
           ...)[[1]], coverage(coverage(rev, extend = ext2, coords = coords, 
           ...))[[1]])
       counts <- .fixCounts(counts, len)
       if (!compress) 
           counts <- decompress(counts)
       counts
   }, chrFilter, chrLen, extend, MoreArgs = list(aligned = aligned, 
       list(...)), SIMPLIFY = FALSE)
3: .local(aligned, chrLen, ...)
2: strandPileup(aln1, chrLen = chr, extend = 1, plot = FALSE)
1: strandPileup(aln1, chrLen = chr, extend = 1, plot = FALSE)

sessioninfo()

R version 3.1.1 (2014-07-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_Singapore.1252  LC_CTYPE=English_Singapore.1252   
[3] LC_MONETARY=English_Singapore.1252 LC_NUMERIC=C                      
[5] LC_TIME=English_Singapore.1252    

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

other attached packages:
 [1] ChIPseqR_1.18.0         nucleR_1.12.0           Biobase_2.24.0         
 [4] Gviz_1.8.4              rtracklayer_1.24.2      PICS_2.8.0             
 [7] PING_2.8.0              chipseq_1.14.0          ShortRead_1.22.0       
[10] GenomicAlignments_1.0.6 Rsamtools_1.16.1        BiocParallel_0.6.1     
[13] BSgenome_1.32.0         Biostrings_2.32.1       XVector_0.4.0          
[16] GenomicRanges_1.16.4    GenomeInfoDb_1.0.2      IRanges_1.22.10        
[19] BiocGenerics_0.10.0     BiocInstaller_1.14.2   

loaded via a namespace (and not attached):
 [1] acepack_1.3-3.3          AnnotationDbi_1.26.1     base64enc_0.1-2         
 [4] BatchJobs_1.4            BBmisc_1.7               biomaRt_2.20.0          
 [7] biovizBase_1.12.3        bitops_1.0-6             brew_1.0-6              
[10] checkmate_1.4            cluster_1.15.2           codetools_0.2-8         
[13] colorspace_1.2-4         DBI_0.3.1                dichromat_2.0-0         
[16] digest_0.6.4             fail_1.2                 fBasics_3010.86         
[19] foreach_1.4.2            foreign_0.8-61           Formula_1.1-2           
[22] GenomicFeatures_1.16.3   HilbertVis_1.22.0        Hmisc_3.14-5            
[25] hwriter_1.3.2            iterators_1.0.7          lattice_0.20-29         
[28] latticeExtra_0.6-26      MASS_7.3-33              matrixStats_0.10.0      
[31] munsell_0.4.2            nnet_7.3-8               plyr_1.8.1              
[34] R.methodsS3_1.6.1        RColorBrewer_1.0-5       Rcpp_0.11.3             
[37] RCurl_1.95-4.3           rpart_4.1-8              RSQLite_0.11.4          
[40] scales_0.2.4             sendmailR_1.2-1          splines_3.1.1           
[43] stabledist_0.6-6         stats4_3.1.1             stringr_0.6.2           
[46] survival_2.37-7          timeDate_3010.98         timeSeries_3010.97      
[49] timsac_1.3.3             tools_3.1.1              VariantAnnotation_1.10.5
[52] XML_3.98-1.1             zlibbioc_1.10.0 

Thanks for reporting the issue. This is now fixed in the development version Bioconductor (but changes won't be visible until the package has been rebuild on the server). Please let me know if you continue to experience problems.