DiffBind: bGain or bLoss parameters in dba.report don't work?
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fleur_p90 • 0
@fleur_p90-10888
Last seen 8 weeks ago
Netherlands

Hi all,

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:
[1] LC_COLLATE=Dutch_Netherlands.1252  LC_CTYPE=Dutch_Netherlands.1252    LC_MONETARY=Dutch_Netherlands.1252
[4] LC_NUMERIC=C                       LC_TIME=Dutch_Netherlands.1252    

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

other attached packages:
 [1] org.Mm.eg.db_3.12.0                       forcats_0.5.1                            
 [3] stringr_1.4.0                             dplyr_1.0.5                              
 [5] purrr_0.3.4                               readr_1.4.0                              
 [7] tidyr_1.1.3                               tibble_3.1.0                             
 [9] ggplot2_3.3.3                             tidyverse_1.3.0                          
[11] diffloop_1.18.0                           TxDb.Mmusculus.UCSC.mm10.knownGene_3.10.0
[13] GenomicFeatures_1.42.2                    AnnotationDbi_1.52.0                     
[15] DiffBind_3.0.14                           SummarizedExperiment_1.20.0              
[17] Biobase_2.50.0                            MatrixGenerics_1.2.1                     
[19] matrixStats_0.58.0                        ChIPseeker_1.26.2                        
[21] GenomicRanges_1.42.0                      GenomeInfoDb_1.26.4                      
[23] IRanges_2.24.1                            S4Vectors_0.28.1                         
[25] BiocGenerics_0.36.0

Any idea what I am doing wrong? Or is there another way to get out only the + or - Fold regions?

Thanks!

Best, Fleur

DiffBind • 256 views
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I found a way to work around this by the following:

OT1.DB_open <- OT1.DB_open[OT1.DB_open$Fold >= 0]

Did the trick. But nevertheless I am curious why the bGain and bLoss don't work as they should

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Rory Stark ★ 4.1k
@rory-stark-5741
Last seen 15 hours ago
CRUK, Cambridge, UK

The bGain and bLoss parameters to dba.report() only have effect when bDB=TRUE, indicating that a report-based DBA object should be returned (rather than a GRanges report). If you want a report-based DBA object, set bDB=TRUE. If you want to filter a regular report based on Fold, you're doing the right thing!

I notice that the help page for dba.report()says that setting bGain or bLoss to TRUE should itself trigger a report-based object, I'll look into either fixing this or updating the documentation.

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Alright, wonderful :) thank you for the reply!

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