dba.count() of DiffBind 3.0 does not have bSubControl parameter
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Entering edit mode
Ha • 0
@Ha-24678
Last seen 7 months ago

Hello,

I'm trying to run DiffBind with my ChIP-seq data. I do not want to subtract control reads from ChIP reads, which should be controlled by bSubControl in dba.count(). However, the parameter does not seem to be available to me. I also did not run grey list analysis.

> ?dba.count

Usage:

     dba.count(DBA, peaks, minOverlap=2, score=DBA_SCORE_NORMALIZED,
               fragmentSize=DBA$config$fragmentSize,
               summits=200, filter=5, bRemoveDuplicates=FALSE, bScaleControl=TRUE,
               mapQCth=DBA$config$mapQCth, filterFun=max, minCount=0,
               bLog=FALSE, bUseSummarizeOverlaps=TRUE,
               readFormat=DBA_READS_DEFAULT, bParallel=DBA$config$RunParallel)

> sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-conda_cos6-linux-gnu (64-bit)
Running under: Ubuntu 16.04 LTS

Matrix products: default
BLAS/LAPACK: /opt/miniconda3/envs/diffbind/lib/libopenblasp-r0.3.10.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=en_US.UTF-8
 [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] forcats_0.5.0               stringr_1.4.0
 [3] purrr_0.3.4                 readr_1.4.0
 [5] tidyr_1.1.2                 tibble_3.0.4
 [7] ggplot2_3.3.3               tidyverse_1.3.0
 [9] dplyr_1.0.2                 DiffBind_3.0.3
[11] SummarizedExperiment_1.20.0 Biobase_2.50.0
[13] MatrixGenerics_1.2.0        matrixStats_0.57.0
[15] GenomicRanges_1.42.0        GenomeInfoDb_1.26.0
[17] IRanges_2.24.0              S4Vectors_0.28.0
[19] BiocGenerics_0.36.0

loaded via a namespace (and not attached):
  [1] readxl_1.3.1             backports_1.2.1          GOstats_2.56.0
  [4] BiocFileCache_1.14.0     plyr_1.8.6               GSEABase_1.52.0
  [7] splines_4.0.2            BiocParallel_1.24.0      amap_0.8-18
 [10] digest_0.6.27            invgamma_1.1             GO.db_3.12.1
 [13] fansi_0.4.1              SQUAREM_2021.1           magrittr_2.0.1
 [16] checkmate_2.0.0          memoise_1.1.0            BSgenome_1.58.0
 [19] base64url_1.4            limma_3.46.0             Biostrings_2.58.0
 [22] annotate_1.68.0          modelr_0.1.8             systemPipeR_1.24.2
 [25] askpass_1.1              bdsmatrix_1.3-4          prettyunits_1.1.1
 [28] jpeg_0.1-8.1             colorspace_2.0-0         rvest_0.3.6
 [31] blob_1.2.1               rappdirs_0.3.1           apeglm_1.12.0
 [34] ggrepel_0.9.0            haven_2.3.1              crayon_1.3.4
 [37] RCurl_1.98-1.2           jsonlite_1.7.2           graph_1.68.0
 [40] genefilter_1.72.0        brew_1.0-6               survival_3.2-7
 [43] VariantAnnotation_1.36.0 glue_1.4.2               gtable_0.3.0
 [46] zlibbioc_1.36.0          XVector_0.30.0           DelayedArray_0.16.0
 [49] V8_3.4.0                 Rgraphviz_2.34.0         scales_1.1.1
 [52] pheatmap_1.0.12          mvtnorm_1.1-1            DBI_1.1.0
 [55] edgeR_3.32.0             Rcpp_1.0.5               xtable_1.8-4
 [58] progress_1.2.2           emdbook_1.3.12           bit_4.0.4
 [61] rsvg_2.1                 AnnotationForge_1.32.0   truncnorm_1.0-8
 [64] httr_1.4.2               gplots_3.1.1             RColorBrewer_1.1-2
 [67] ellipsis_0.3.1           pkgconfig_2.0.3          XML_3.99-0.5
 [70] dbplyr_2.0.0             locfit_1.5-9.4           tidyselect_1.1.0
 [73] rlang_0.4.10             AnnotationDbi_1.52.0     cellranger_1.1.0
 [76] munsell_0.5.0            tools_4.0.2              cli_2.2.0
 [79] generics_0.1.0           RSQLite_2.2.2            broom_0.7.3
 [82] yaml_2.2.1               fs_1.5.0                 bit64_4.0.5
 [85] caTools_1.18.1           RBGL_1.66.0              xml2_1.3.2
 [88] biomaRt_2.46.0           rstudioapi_0.13          compiler_4.0.2
 [91] curl_4.3                 png_0.1-7                reprex_0.3.0
 [94] stringi_1.5.3            ps_1.5.0                 GenomicFeatures_1.42.0
 [97] lattice_0.20-41          Matrix_1.3-2             vctrs_0.3.6
[100] pillar_1.4.7             lifecycle_0.2.0          data.table_1.13.6
[103] bitops_1.0-6             irlba_2.3.3              rtracklayer_1.50.0
[106] R6_2.5.0                 latticeExtra_0.6-29      hwriter_1.3.2
[109] ShortRead_1.48.0         KernSmooth_2.23-18       MASS_7.3-53
[112] gtools_3.8.2             assertthat_0.2.1         openssl_1.4.3
[115] Category_2.56.0          rjson_0.2.20             withr_2.3.0
[118] GenomicAlignments_1.26.0 batchtools_0.9.15        Rsamtools_2.6.0
[121] GenomeInfoDbData_1.2.4   hms_0.5.3                grid_4.0.2
[124] DOT_0.1                  coda_0.19-4              GreyListChIP_1.22.0
[127] ashr_2.2-47              mixsqp_0.3-43            bbmle_1.0.23.1
[130] lubridate_1.7.9.2        numDeriv_2016.8-1.1

I really appreciate any help. Thank you!

DiffBind • 200 views
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1
Entering edit mode
Rory Stark ★ 4.1k
@rory-stark-5741
Last seen 1 day ago
CRUK, Cambridge, UK

The bSubControl parameter has been restored to dba.count(), you just need to update. Current version is DiffBind_3.0.12.

New behavior is for bSubControl to be TRUE by default if there are no greylists, so as you expect, you'll need to set it to FALSE.

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