Mistake in `BSseq` constructor?

rcavalcante commented 5 years ago

Hello,

I'm trying to get the code for methylSig in working order with the Bioc 3.8 and devel versions of bsseq and I'm running into a problem I didn't have with previous versions.

Namely,

library(bsseq)

gr =GRanges(
    seqnames = c('chr21','chr21','chr21'),
    ranges = IRanges(start = c(1,3,5), end = c(1,3,5)),
    strand = '*'
)

m = matrix(
    data = c(34,10,0,300,87,434), 
    nrow = 3, ncol = 2,
    dimnames = list(NULL, c('test_1','test_2')))

cov = matrix(
    data = c(34,10,0,300,96,458), 
    nrow = 3, ncol = 2,
    dimnames = list(NULL, c('test_1','test_2')))

pData = data.frame(
    Sample_Name = c('test_1','test_2'),
    Group = factor(1,0),
    row.names = c('test_1','test_2')
)

bs = bsseq::BSseq(gr = gr, M = m, Cov = cov, pData = pData)

Gives the following error despite the rownames of pData being correct relative to the M and Cov parameters:

Error in `rownames<-`(`*tmp*`, value = .get_colnames_from_assays(assays)) : 
  invalid rownames length

I've tracked down the problem to this block of the constructor (lines 91-111 of BSseq-class.R):

    # Process 'sampleNames' and 'pData'.
    if (is.null(sampleNames)) {
        if (is.null(pData)) {
            # BSseq object will have no colnames.
            pData <- S4Vectors:::new_DataFrame(nrows = ncol(M))
        } else {
            # BSseq object will have 'sampleNames' as colnames.
            pData <- DataFrame(row.names = sampleNames)
        }
    } else {
        if (is.null(pData)) {
            # BSseq object will have 'sampleNames' as colnames.
            pData <- DataFrame(row.names = sampleNames)
        } else {
            if (is.null(rownames(pData))) {
                rownames(pData) <- sampleNames
            } else {
                stopifnot(identical(rownames(pData), sampleNames))
            }
        }
    }

The small example I've given above has NULL sampleNames but non-NULL pData, so it tries to run pData <- DataFrame(row.names = sampleNames), which obliterates the pData I've passed and causes the invalid rownames error.

I think, at least. Please let me know if I've misunderstood or you can't reproduce with the example above. Thanks in advance!

Here is my sessionInfo(), I'm running in the Bioc 3.8 release Docker image with updated packages:

R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 9 (stretch)

Matrix products: default
BLAS: /usr/lib/openblas-base/libblas.so.3
LAPACK: /usr/lib/libopenblasp-r0.2.19.so

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=C             
 [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  stats4    stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] SummarizedExperiment_1.12.0 DelayedArray_0.8.0         
 [3] BiocParallel_1.16.5         matrixStats_0.54.0         
 [5] Biobase_2.42.0              GenomicRanges_1.34.0       
 [7] GenomeInfoDb_1.18.1         IRanges_2.16.0             
 [9] S4Vectors_0.20.1            BiocGenerics_0.28.0        
[11] methylSig_0.6.0             testthat_2.0.1             
[13] BiocManager_1.30.4         

loaded via a namespace (and not attached):
 [1] DSS_2.30.1                    bitops_1.0-6                 
 [3] fs_1.2.6                      usethis_1.4.0                
 [5] devtools_2.0.1                bit64_0.9-7                  
 [7] bsseq_1.18.0                  progress_1.2.0               
 [9] httr_1.4.0                    rprojroot_1.3-2              
[11] tools_3.5.1                   backports_1.1.3              
[13] R6_2.3.0                      HDF5Array_1.10.1             
[15] DBI_1.0.0                     lazyeval_0.2.1               
[17] colorspace_1.4-0              permute_0.9-4                
[19] withr_2.1.2                   tidyselect_0.2.5             
[21] prettyunits_1.0.2             processx_3.2.1               
[23] bit_1.1-14                    compiler_3.5.1               
[25] cli_1.0.1                     desc_1.2.0                   
[27] rtracklayer_1.42.1            scales_1.0.0                 
[29] readr_1.3.1                   callr_3.1.1                  
[31] stringr_1.3.1                 digest_0.6.18                
[33] Rsamtools_1.34.1              R.utils_2.7.0                
[35] XVector_0.22.0                pkgconfig_2.0.2              
[37] htmltools_0.3.6               sessioninfo_1.1.1            
[39] limma_3.38.3                  BSgenome_1.50.0              
[41] regioneR_1.14.0               rlang_0.3.1                  
[43] rstudioapi_0.9.0              RSQLite_2.1.1                
[45] DelayedMatrixStats_1.4.0      shiny_1.2.0                  
[47] bindr_0.1.1                   gtools_3.8.1                 
[49] R.oo_1.22.0                   dplyr_0.7.8                  
[51] RCurl_1.95-4.11               magrittr_1.5                 
[53] GenomeInfoDbData_1.2.0        Matrix_1.2-15                
[55] Rhdf5lib_1.4.2                Rcpp_1.0.0                   
[57] munsell_0.5.0                 R.methodsS3_1.7.1            
[59] stringi_1.2.4                 yaml_2.2.0                   
[61] zlibbioc_1.28.0               rhdf5_2.26.2                 
[63] pkgbuild_1.0.2                plyr_1.8.4                   
[65] AnnotationHub_2.14.3          grid_3.5.1                   
[67] blob_1.1.1                    promises_1.0.1               
[69] crayon_1.3.4                  lattice_0.20-38              
[71] Biostrings_2.50.2             GenomicFeatures_1.34.3       
[73] hms_0.4.2                     locfit_1.5-9.1               
[75] ps_1.3.0                      pillar_1.3.1                 
[77] boot_1.3-20                   reshape2_1.4.3               
[79] biomaRt_2.38.0                pkgload_1.0.2                
[81] XML_3.98-1.16                 glue_1.3.0                   
[83] annotatr_1.8.0                data.table_1.12.0            
[85] remotes_2.0.2                 httpuv_1.4.5.1               
[87] gtable_0.2.0                  purrr_0.3.0                  
[89] assertthat_0.2.0              ggplot2_3.1.0                
[91] mime_0.6                      xtable_1.8-3                 
[93] later_0.7.5                   tibble_2.0.1                 
[95] GenomicAlignments_1.18.1      AnnotationDbi_1.44.0         
[97] memoise_1.1.0                 bindrcpp_0.2.2               
[99] interactiveDisplayBase_1.20.0