I am performing the package diffbind and at the end I would like to make two separate files for the regions that are open and closed (I am analyzing ATAC seq data). However, setting the parameter bGain = TRUE or bLoss = TRUE doesn't change anything....
Here's my code
OT1.DB_sign <- dba.report(OT1) OT1.DB_open <- dba.report(OT1, bAll = FALSE, bGain = TRUE) OT1.DB_close <- dba.report(OT1, bAll = FALSE, bLoss = TRUE) # output in the console: > OT1.DB_sign GRanges object with 2566 ranges and 6 metadata columns: > OT1.DB_open GRanges object with 2566 ranges and 6 metadata columns: > OT1.DB_close GRanges object with 2566 ranges and 6 metadata columns: # Output of all three files is the same and I can see in the Fold column both negative and positive values > sessionInfo() R version 4.0.4 (2021-02-15) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19042) Matrix products: default locale:  LC_COLLATE=Dutch_Netherlands.1252 LC_CTYPE=Dutch_Netherlands.1252 LC_MONETARY=Dutch_Netherlands.1252  LC_NUMERIC=C LC_TIME=Dutch_Netherlands.1252 attached base packages:  parallel stats4 stats graphics grDevices utils datasets methods base other attached packages:  org.Mm.eg.db_3.12.0 forcats_0.5.1  stringr_1.4.0 dplyr_1.0.5  purrr_0.3.4 readr_1.4.0  tidyr_1.1.3 tibble_3.1.0  ggplot2_3.3.3 tidyverse_1.3.0  diffloop_1.18.0 TxDb.Mmusculus.UCSC.mm10.knownGene_3.10.0  GenomicFeatures_1.42.2 AnnotationDbi_1.52.0  DiffBind_3.0.14 SummarizedExperiment_1.20.0  Biobase_2.50.0 MatrixGenerics_1.2.1  matrixStats_0.58.0 ChIPseeker_1.26.2  GenomicRanges_1.42.0 GenomeInfoDb_1.26.4  IRanges_2.24.1 S4Vectors_0.28.1  BiocGenerics_0.36.0
Any idea what I am doing wrong? Or is there another way to get out only the + or - Fold regions?