This is a question on the "summit" function in DiffBind.
I would like to generate a set of consensus peaks with width of 201bp, centered around the peak summit. The codes I used were:
dba.object <- dba( sampleSheet = metadata, peakCaller="bed", scoreCol=5, bRemoveM=TRUE, bLowerScoreBetter=TRUE, config=data.frame(bUsePval=TRUE), bCorPlot=FALSE) count.data <- dba.count( dba.object, minOverlap=1, score=DBA_SCORE_READS, bCorPlot=FALSE, summits=100, bUseSummarizeOverlaps=F )
To retrieve the count matrix, along with the peak coordinates, I used:
count.matrix <- dba.peakset(count.data, bRetrieve=T, DataType=DBA_DATA_FRAME)
However, I realized that there were a very small set of peaks larger than 201bp in the final consensus peak set (approximately 5% of the consensus peak set). I am unable to figure out why this would be so and would appreciate any assistance on this.
My saved dba.object can be retrieved from here: https://www.dropbox.com/s/eh3qpanm0lgdn6f/dba_object_debug.rds?dl=0
The DiffBind version I used was 2.2.9
sessionInfo() R version 3.3.2 (2016-10-31) Platform: x86_64-centos-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core) locale:  LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C  LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8  LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8  LC_PAPER=en_US.UTF-8 LC_NAME=C  LC_ADDRESS=C LC_TELEPHONE=C  LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages:  parallel stats4 stats graphics grDevices utils datasets  methods base other attached packages:  DiffBind_2.2.9 SummarizedExperiment_1.4.0  Biobase_2.34.0 GenomicRanges_1.26.2  GenomeInfoDb_1.10.2 IRanges_2.8.0  S4Vectors_0.14.4 BiocGenerics_0.22.0 loaded via a namespace (and not attached):  Rcpp_0.12.11 locfit_1.5-9.1 lattice_0.20-34  GO.db_3.4.0 Rsamtools_1.26.1 Biostrings_2.42.1  gtools_3.5.0 assertthat_0.2.0 digest_0.6.12  R6_2.2.2 plyr_1.8.4 BatchJobs_1.6  backports_1.0.5 ShortRead_1.32.1 RSQLite_1.0.0  ggplot2_2.2.1 gplots_3.0.1 zlibbioc_1.20.0  rlang_0.1.1 GenomicFeatures_1.26.2 lazyeval_0.2.0  annotate_1.52.1 gdata_2.18.0 Matrix_1.2-7.1  checkmate_1.8.2 systemPipeR_1.8.1 GOstats_2.40.0  splines_3.3.2 BiocParallel_1.8.1 stringr_1.2.0  pheatmap_1.0.8 RCurl_1.95-4.8 biomaRt_2.30.0  munsell_0.4.3 sendmailR_1.2-1 rtracklayer_1.34.1  pkgconfig_2.0.1 base64enc_0.1-3 BBmisc_1.11  fail_1.3 tibble_1.3.3 edgeR_3.16.5  XML_3.98-1.5 AnnotationForge_1.16.0 dplyr_0.7.1  GenomicAlignments_1.10.0 bitops_1.0-6 grid_3.3.2  RBGL_1.50.0 xtable_1.8-2 GSEABase_1.36.0  gtable_0.2.0 DBI_0.5-1 magrittr_1.5  scales_0.4.1 graph_1.52.0 KernSmooth_2.23-15  amap_0.8-14 stringi_1.1.5 XVector_0.14.0  hwriter_1.3.2 genefilter_1.56.0 bindrcpp_0.2  limma_3.30.8 latticeExtra_0.6-28 brew_1.0-6  rjson_0.2.15 RColorBrewer_1.1-2 tools_3.3.2  glue_1.1.1 Category_2.40.0 survival_2.39-5  AnnotationDbi_1.36.0 colorspace_1.3-2 caTools_1.17.1  bindr_0.1