DiffBind reporting error
1
0
Entering edit mode
Bei Jun • 0
@bei-jun-24172
Last seen 6 months ago

Hi,

I am using DiffBind (development version 3.0.5) to identify differential open chromatin regions in two cell groups (control vs treated) using ATAC-seq data.

My dba configuration is as follows:

open_region_config <- data.frame(RunParallel=T,
                        reportInit="DBA",
                        DataType=DBA_DATA_GRANGES, 
                        minQCth=15, 
                        fragmentSize=0, #" If set to zero, the read size indicated in the BAM/BED file will be used."
                        bCorPlot=F,
                        th=0.05,
                        bUsePval=F,
                        doGreylist=F)

dba.analyze():

open_region_24h <- dba(sampleSheet="/Volumes/Samsung_T5/Duke-NUS/inhouse_ATACseq/samples_24h.csv",
                   config=open_region_config,
                   peakCaller="bed") %>%
  dba.count(score = DBA_SCORE_READS,
            summits = 100) %>%
  dba.contrast(minMembers = 2) %>%
  dba.analyze(bBlacklist = TRUE,
              bParallel = TRUE,
              bReduceObjects = TRUE)

The above code was processed and completed without errors.

However, when I was trying to get the results from the dba.analyze() object using dba.report():

or_24h_FDR10.DB <- dba.report(open_region_24h,
                              th=0.1)

I encountered the following error:

Error in .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges") : In range 2160: at least two out of 'start', 'end', and 'width', must be supplied.

  1. .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges").
  2. solveUserSEW0(start = start, end = end, width = width).
  3. IRanges(peaks[, 2], width = peaks[, 3] - peaks[, 2] + 1, names = rownames(peaks)).
  4. GRanges(Rle(factor(peaks[, 1], levels = chrmap)), IRanges(peaks[, 2], width = peaks[, 3] - peaks[, 2] + 1, names = rownames(peaks)), strand <- Rle("*", length(seqnames))).
  5. pv.peaks2DataType(res, DataType).
  6. dba.report(open_region_24h, th = 0.1).

I tried to see if any range values in the 2160th row is missing but couldn't find any:

open_region_24h$peaks[[1]][2160,] #also [[2]], [[3]], and [[4]]

- seqnames start end Score RPKM Reads cRPKM cReads
2160 chr1 150697185 150697385 99 8.309346 99 0 0.

Does anyone know how to fix this? I would appreciate any suggestions on this.

Thank you in advance.

Bei Jun

> sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.7

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] edgeR_3.30.3                limma_3.44.3                dplyr_1.0.2                 DiffBind_3.0.5             
 [5] SummarizedExperiment_1.18.2 DelayedArray_0.14.1         matrixStats_0.57.0          Biobase_2.48.0             
 [9] GenomicRanges_1.40.0        GenomeInfoDb_1.24.2         IRanges_2.22.2              S4Vectors_0.26.1           
[13] BiocGenerics_0.34.0        

loaded via a namespace (and not attached):
  [1] backports_1.2.0          GOstats_2.54.0           BiocFileCache_1.12.1     plyr_1.8.6               GSEABase_1.50.1         
  [6] splines_4.0.2            BiocParallel_1.22.0      ggplot2_3.3.2            amap_0.8-18              digest_0.6.27           
 [11] invgamma_1.1             htmltools_0.5.0          GO.db_3.11.4             SQUAREM_2020.5           magrittr_1.5            
 [16] checkmate_2.0.0          memoise_1.1.0            BSgenome_1.56.0          base64url_1.4            Biostrings_2.56.0       
 [21] annotate_1.66.0          systemPipeR_1.22.0       askpass_1.1              bdsmatrix_1.3-4          prettyunits_1.1.1       
 [26] jpeg_0.1-8.1             colorspace_2.0-0         blob_1.2.1               rappdirs_0.3.1           apeglm_1.10.0           
 [31] ggrepel_0.8.2            xfun_0.19                crayon_1.3.4             RCurl_1.98-1.2           jsonlite_1.7.1          
 [36] graph_1.66.0             genefilter_1.70.0        brew_1.0-6               survival_3.2-7           VariantAnnotation_1.34.0
 [41] glue_1.4.2               gtable_0.3.0             zlibbioc_1.34.0          XVector_0.28.0           V8_3.4.0                
 [46] Rgraphviz_2.32.0         scales_1.1.1             pheatmap_1.0.12          mvtnorm_1.1-1            DBI_1.1.0               
 [51] Rcpp_1.0.5               xtable_1.8-4             progress_1.2.2           emdbook_1.3.12           bit_4.0.4               
 [56] rsvg_2.1                 AnnotationForge_1.30.1   truncnorm_1.0-8          httr_1.4.2               gplots_3.1.0            
 [61] RColorBrewer_1.1-2       ellipsis_0.3.1           pkgconfig_2.0.3          XML_3.99-0.5             dbplyr_2.0.0            
 [66] locfit_1.5-9.4           tidyselect_1.1.0         rlang_0.4.8              AnnotationDbi_1.50.3     munsell_0.5.0           
 [71] tools_4.0.2              generics_0.1.0           RSQLite_2.2.1            evaluate_0.14            stringr_1.4.0           
 [76] yaml_2.2.1               knitr_1.30               bit64_4.0.5              caTools_1.18.0           purrr_0.3.4             
 [81] RBGL_1.64.0              xml2_1.3.2               biomaRt_2.44.4           compiler_4.0.2           rstudioapi_0.13         
 [86] curl_4.3                 png_0.1-7                statmod_1.4.35           geneplotter_1.66.0       tibble_3.0.4            
 [91] stringi_1.5.3            GenomicFeatures_1.40.1   lattice_0.20-41          Matrix_1.2-18            vctrs_0.3.4             
 [96] pillar_1.4.6             lifecycle_0.2.0          irlba_2.3.3              data.table_1.13.2        bitops_1.0-6            
[101] rtracklayer_1.48.0       R6_2.5.0                 latticeExtra_0.6-29      hwriter_1.3.2            ShortRead_1.46.0        
[106] KernSmooth_2.23-18       MASS_7.3-53              gtools_3.8.2             assertthat_0.2.1         DESeq2_1.28.1           
[111] openssl_1.4.3            Category_2.54.0          rjson_0.2.20             withr_2.3.0              GenomicAlignments_1.24.0
[116] batchtools_0.9.14        Rsamtools_2.4.0          GenomeInfoDbData_1.2.3   hms_0.5.3                grid_4.0.2              
[121] DOT_0.1                  coda_0.19-4              rmarkdown_2.5            GreyListChIP_1.20.0      ashr_2.2-47             
[126] mixsqp_0.3-43            bbmle_1.0.23.1           numDeriv_2016.8-1.1
DiffBind • 261 views
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0
Entering edit mode
Rory Stark ★ 3.9k
@rory-stark-5741
Last seen 1 day ago
CRUK, Cambridge, UK

This should be fixed in the current Release, DiffBind_3.0.6, available as of today on all platforms.

You are using the Release version (3.0). I’ll be rolling the fix into the Development version as well in the next couple of days.You may need to update to R_4.0.3 to get the current versions of everything, particularly GenomicRanges_1.42.0.

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Entering edit mode

Hi, I also have the reported problem, although my env is up-to-data (R 4.0.3, GenomicRanges_1.42.0, DiffBind_3.0.13). In particular the problem seems limited to edger, while it works fine with DESeq2. Any idea of why? Ivan

# edgeR
dbind.report.edger <- dba.report(DBA = dbind_de, contrast = 1, method = DBA_EDGER, th = fdr_thr, fold = lfc_thr)

Error in .Call2("C_solve_user_SEW0", start, end, width, PACKAGE = "IRanges") : In range 1222: at least two out of 'start', 'end', and 'width', must be supplied.

# DESeq2
dbind.report.deseq2 <- dba.report(DBA = dbind_de, contrast = 1, method = DBA_DESEQ2, th = fdr_thr, fold = lfc_thr)

sessionInfo() R version 4.0.3 (2020-10-10) Platform: x86_64-conda-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)

Matrix products: default BLAS/LAPACK: /opt/common/tools/ric.tiget/anaconda3/envs/atac/lib/libopenblasp-r0.3.12.so

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C 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 LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets methods base

other attached packages: [1] openxlsx_4.2.3 DiffBind_3.0.13 SummarizedExperiment_1.20.0 Biobase_2.50.0
[5] MatrixGenerics_1.2.1 matrixStats_0.58.0 GenomicRanges_1.42.0 GenomeInfoDb_1.26.2
[9] IRanges_2.24.1 S4Vectors_0.28.1 BiocGenerics_0.36.0

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Entering edit mode

If you could give me access to your dbind_de object, I can have a look at what is going on. it would help to see the sequence of calls you used to generate it up tot he report as well.

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