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Question: DiffBind broad and narrow peak identification
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gravatar for reubenmcgregor88
10 weeks ago by
reubenmcgregor880 wrote:

Hi, 

I have histone, broad-peak data, however some of the peaks are actually rather narrow. So what I can see happening is that the broader peaks are being nicely identified as differentially expressed by diffbind, but the narrow peaks which seem highly up-regulated (with big fold changes) are not reaching FDR significance. My interpretation is that there are less counts compared to broad peaks.

The code I used for differential peak analysis is as follows:

> samples <- dba(sampleSheet=diffbind_samples, peakCaller = "bed", peakFormat = "bed")
> samples_counts <- dba.count(samples)
> samples_counts <- dba.contrast(samples_counts, categories=DBA_CONDITION, minMembers=2)
> samples_counts <- dba.analyze(samples_counts)

I wonder whether this is something you have come across before? I have tried playing around with "summits" function and "bFullLibrarySize" but not sure how I can best tackle this problem? To give you an idea here is the readout for one of the narrow peaks in question:

Chr Start End Conc Conc_vitd Conc_eth Fold p-value FDR Called1 Called2 k27acvitd1 k27acvitd2 k27aceth1 k27aceth2  
chr2 102918383 102918857 7.02 7.79 5.23 2.55 0.00444 0.513 2 1 217.33 225.1 69.3 6  

So the eth condition goes from 69.3 and 6 to 217.33 and 225.1

and this is one of the broader peaks which is identified as differentially expressed:

Chr Start End Conc Conc_vitd Conc_eth Fold p-value FDR Called1 Called2 k27acvitd1 k27acvitd2 k27aceth1 k27aceth2
chr2 204693199 204696874 9.14 9.92 7.33 2.59 3.60E-06 0.00245 2 2 935.67 1004.41 256.79 65

 Here is my sample sheet:

SampleID Tissue Factor Condition Treatment Replicate bamReads ControlID bamControl Peaks PeakCaller
                       

1

k27acvitd1

cd4

k27ac

vitd

a

1

Bowtie_1_27Ac_VitD.bam

natinput

Bowtie_1_NInput_Eth.bam

27ac.vitD.don1.peaks.styleregion.250bp.mindist5kb_diffbind.bed

bed

2

k27acvitd2

cd4

k27ac

vitd

a

2

Bowtie_2_27Ac_VitD.bam

natinput

Bowtie_1_NInput_Eth.bam

27ac.vitD.don2.peaks.styleregion.250bp.mindist5kb.diffbind.bed

bed

3

k27aceth1

cd4

k27ac

eth

a

1

Bowtie_1_27Ac_Eth.bam

natinput

Bowtie_1_NInput_Eth.bam

27ac.eth.don1.peaks.styleregion.250bp.mindist5kb_diffbind.bed

bed

4

k27aceth2

cd4

k27ac

eth

a

2

Bowtie_2_27Ac_Eth.bam

natinput

Bowtie_1_NInput_Eth.bam

27ac.eth.don2.peaks.styleregion.250bp.mindist5kb.diffbind.bed

bed

sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

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

other attached packages:
 [1] readr_1.1.1                DiffBind_2.4.8             SummarizedExperiment_1.6.3
 [4] DelayedArray_0.2.7         matrixStats_0.52.2         Biobase_2.36.2            
 [7] GenomicRanges_1.28.4       GenomeInfoDb_1.12.2        IRanges_2.10.2            
[10] S4Vectors_0.14.3           BiocGenerics_0.22.0       

loaded via a namespace (and not attached):
  [1] Category_2.42.1          bitops_1.0-6             bit64_0.9-7              RColorBrewer_1.1-2      
  [5] httr_1.3.1               tools_3.4.1              backports_1.1.0          R6_2.2.2                
  [9] rpart_4.1-11             KernSmooth_2.23-15       Hmisc_4.0-3              DBI_0.7                 
 [13] lazyeval_0.2.0           colorspace_1.3-2         nnet_7.3-12              gridExtra_2.2.1         
 [17] DESeq2_1.16.1            bit_1.1-12               compiler_3.4.1           sendmailR_1.2-1         
 [21] graph_1.54.0             htmlTable_1.9            plotly_4.7.1             rtracklayer_1.36.4      
 [25] caTools_1.17.1           scales_0.5.0             checkmate_1.8.3          BatchJobs_1.6           
 [29] genefilter_1.58.1        RBGL_1.52.0              stringr_1.2.0            digest_0.6.12           
 [33] Rsamtools_1.28.0         foreign_0.8-69           AnnotationForge_1.18.1   XVector_0.16.0          
 [37] base64enc_0.1-3          pkgconfig_2.0.1          htmltools_0.3.6          limma_3.32.5            
 [41] htmlwidgets_0.9          rlang_0.1.2              RSQLite_2.0              BBmisc_1.11             
 [45] GOstats_2.42.0           bindr_0.1                hwriter_1.3.2            jsonlite_1.5            
 [49] BiocParallel_1.10.1      gtools_3.5.0             acepack_1.4.1            dplyr_0.7.2             
 [53] RCurl_1.95-4.8           magrittr_1.5             GO.db_3.4.1              GenomeInfoDbData_0.99.0 
 [57] Formula_1.2-2            Matrix_1.2-11            Rcpp_0.12.12             munsell_0.4.3           
 [61] stringi_1.1.5            edgeR_3.18.1             zlibbioc_1.22.0          fail_1.3                
 [65] gplots_3.0.1             plyr_1.8.4               grid_3.4.1               blob_1.1.0              
 [69] ggrepel_0.6.5            gdata_2.18.0             lattice_0.20-35          Biostrings_2.44.2       
 [73] splines_3.4.1            GenomicFeatures_1.28.4   annotate_1.54.0          hms_0.3                 
 [77] locfit_1.5-9.1           knitr_1.17               rjson_0.2.15             systemPipeR_1.10.2      
 [81] geneplotter_1.54.0       biomaRt_2.32.1           XML_3.98-1.9             glue_1.1.1              
 [85] ShortRead_1.34.0         latticeExtra_0.6-28      data.table_1.10.4        gtable_0.2.0            
 [89] purrr_0.2.3              tidyr_0.7.0              amap_0.8-14              assertthat_0.2.0        
 [93] ggplot2_2.2.1            xtable_1.8-2             survival_2.41-3          viridisLite_0.2.0       
 [97] pheatmap_1.0.8           tibble_1.3.4             GenomicAlignments_1.12.2 AnnotationDbi_1.38.2    
[101] memoise_1.1.0            bindrcpp_0.2             cluster_2.0.6            brew_1.0-6              
[105] GSEABase_1.38.1   

 
ADD COMMENTlink modified 8 weeks ago by Rory Stark2.1k • written 10 weeks ago by reubenmcgregor880
1
gravatar for Rory Stark
8 weeks ago by
Rory Stark2.1k
CRUK, Cambridge, UK
Rory Stark2.1k wrote:

In the example you show, while the fold-change difference is similar, there is quite a bit more variance in the second sample group, so it may not be surprising that it gets a higher p-value that gets more drastically adjusted by the FDR correction.

You mention trying the summits option in dba.count(), how did that change things? That's what I would try -- see my recent discussion of this here: A: How to select summit size for histone ChiP-Seq in Diffbind

-Rory

ADD COMMENTlink written 8 weeks ago by Rory Stark2.1k
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