Hello,

I'm using DiffBind to identify differential binding affinity of histone marks H3k27ac between two conditions. I set the summits parameter in dba.count(), but the resulting peaks still have different widths. For example:

seqname  start             end                width    
6         29330809        29331809          1001
9         43674228        43675228          1001
1         84561539        84563500          1962

Can you guys help explain this to me? Thank you a lot! The following is my code:

enhancer <- dba(sampleSheet = sample, peakFormat = "narrow", scoreCol = 9)
enhancer <- dba.count(enhancer, minOverlap = 4,  summits = 500, score=DBA_SCORE_TMM_MINUS_FULL)
enhancer <- dba.contrast(enhancer, enhancer$masks$cond1, enhancer$masks$cond2, "cond1", "con2")
enhancer <- dba.analyze(enhancer, method=DBA_ALL_METHODS, bSubControl = FALSE, bFullLibrarySize = FALSE, bTagwise = TRUE)
enhancer.DB <- dba.report(enhancer, method=DBA_EDGER)

This is my session info:

> sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux

Matrix products: default
BLAS/LAPACK: /path/to/lib/libopenblas_haswell-r0.3.4.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] DiffBind_2.14.0             SummarizedExperiment_1.16.1
 [3] DelayedArray_0.12.3         BiocParallel_1.20.1
 [5] matrixStats_0.56.0          Biobase_2.46.0
 [7] GenomicRanges_1.38.0        GenomeInfoDb_1.22.1
 [9] IRanges_2.20.2              S4Vectors_0.24.4
[11] BiocGenerics_0.32.0

loaded via a namespace (and not attached):
  [1] Category_2.52.1          bitops_1.0-6             bit64_0.9-7
  [4] RColorBrewer_1.1-2       progress_1.2.2           httr_1.4.1
  [7] Rgraphviz_2.30.0         backports_1.1.6          tools_3.6.0
 [10] R6_2.4.1                 KernSmooth_2.23-16       DBI_1.1.0
 [13] colorspace_1.4-1         withr_2.1.2              tidyselect_1.0.0
 [16] prettyunits_1.1.1        bit_1.1-15.2             curl_4.3
 [19] compiler_3.6.0           graph_1.64.0             cli_2.0.2
 [22] rtracklayer_1.46.0       checkmate_2.0.0          caTools_1.18.0
 [25] scales_1.1.0             genefilter_1.68.0        RBGL_1.62.1
 [28] askpass_1.1              rappdirs_0.3.1           stringr_1.4.0
 [31] digest_0.6.25            Rsamtools_2.2.3          AnnotationForge_1.28.0
 [34] XVector_0.26.0           jpeg_0.1-8.1             pkgconfig_2.0.3
 [37] BSgenome_1.54.0          dbplyr_1.4.2             limma_3.42.2
 [40] rlang_0.4.5              RSQLite_2.2.0            GOstats_2.52.0
 [43] hwriter_1.3.2            gtools_3.8.2             dplyr_0.8.5
 [46] VariantAnnotation_1.32.0 RCurl_1.98-1.1           magrittr_1.5
 [49] GO.db_3.10.0             GenomeInfoDbData_1.2.2   Matrix_1.2-18
 [52] Rcpp_1.0.4.6             munsell_0.5.0            fansi_0.4.1
 [55] lifecycle_0.2.0          yaml_2.2.1               stringi_1.4.6
 [58] edgeR_3.28.1             zlibbioc_1.32.0          gplots_3.0.3
 [61] BiocFileCache_1.10.2     grid_3.6.0               blob_1.2.1
 [64] ggrepel_0.8.2            gdata_2.18.0             crayon_1.3.4
 [67] lattice_0.20-41          splines_3.6.0            Biostrings_2.54.0
 [70] annotate_1.64.0          GenomicFeatures_1.38.2   hms_0.5.3
 [73] batchtools_0.9.13        locfit_1.5-9.4           pillar_1.4.3
 [76] rjson_0.2.20             systemPipeR_1.20.0       base64url_1.4
 [79] biomaRt_2.42.1           XML_3.99-0.3             glue_1.4.0
 [82] ShortRead_1.44.3         latticeExtra_0.6-29      data.table_1.12.8
 [85] vctrs_0.2.4              png_0.1-7                gtable_0.3.0
 [88] openssl_1.4.1            purrr_0.3.3              amap_0.8-18
 [91] assertthat_0.2.1         ggplot2_3.3.0            xtable_1.8-4
 [94] survival_3.1-12          pheatmap_1.0.12          tibble_3.0.0
 [97] GenomicAlignments_1.22.1 AnnotationDbi_1.48.0     memoise_1.1.0
[100] brew_1.0-6               ellipsis_0.3.0           GSEABase_1.48.0