Question: diffbind plotVenn by Factor
0
gravatar for theodore.georgomanolis
17 days ago by
Germany

Hi all, so I got the following from ATAC-seq samples

ATACseqGoett_peaks

11 Samples, 47306 sites in matrix:
                ID      Tissue   Factor Replicate Caller Intervals FRiP
1     Cell1px8old  epithelial   Cell1         1 counts     47306 0.19
2       Cell1_3rd  epithelial   Cell1         2 counts     47306 0.18
3    Cell1px11new  epithelial   Cell1         3 counts     47306 0.13
4       Cell2_3rd  epithelial   Cell2         2 counts     47306 0.08
5     Cell2px18_A  epithelial   Cell2         3 counts     47306 0.13
6     Cell2px18_B  epithelial   Cell2         4 counts     47306 0.11
7  Cellca2px17new mesenchymal Cellca2         1 counts     47306 0.08
8     Cellca2_3rd mesenchymal Cellca2         2 counts     47306 0.16
9      Cellc1px8old mesenchymal    Cellc1         1 counts     47306 0.10
10  Cellc1px8oldfew mesenchymal    Cellc1         2 counts     47306 0.10
11       Cellc1_3rd mesenchymal    Cellc1         3 counts     47306 0.13

7 Contrasts:
      Group1 Members1      Group2 Members2 DB.edgeR DB.DESeq2
1     Cell1        3      Cell2        3    16792      9615
2     Cell1        3    Cellca2        2    16666      7530
3     Cell1        3       Cellc1        3    15889     10643
4     Cell2        3    Cellca2        2    10799      2439
5     Cell2        3       Cellc1        3     8969      3720
6   Cellca2        2       Cellc1        3     1136       287
7 epithelial        6 mesenchymal        5     5869      6248

and I would like to plot a 4 way venn based on factor. Is it possible? EDIT to clarify things I want to plot in a Venn the calculated overlap (dba.overlap) of each factor, and then apply the dba.plotvenn in all four FACTORS.

I do not want to do it by bedtools if possible. Thank you in advance

diffbind plotvenn • 51 views
ADD COMMENTlink modified 13 days ago by Rory Stark2.8k • written 17 days ago by theodore.georgomanolis0
Answer: diffbind plotVenn by Factor
0
gravatar for Rory Stark
13 days ago by
Rory Stark2.8k
CRUK, Cambridge, UK
Rory Stark2.8k wrote:

In the help page for dba.plotVenn(), there is an example of how to do this.

In that case, it is based on tissue type (cell line). First the consensus peaks are added of reach tissue type, then the four-way Venn is plotted. This should be done on the peaks themselves, before the counting step. Here is the example from the help page:

#4-way overlap
data(tamoxifen_peaks)
tamoxifen <- dba.peakset(tamoxifen, consensus=DBA_TISSUE)
dba.plotVenn(tamoxifen,tamoxifen$masks$Consensus,main="Tissue consensus overlaps")

In your case, you would change DBA_TISSUE to DBA_FACTOR.

ADD COMMENTlink written 13 days ago by Rory Stark2.8k

Hi Rory,

I did try that and I get the following:

> dba.plotVenn(CHIP_seq_Goett_peaks_ALL, consensus=DBA_FACTOR)
Error in dba.plotVenn(CHIP_seq_Goett_peaks_ALL, consensus = DBA_FACTOR) : 
  unused argument (consensus = DBA_FACTOR)

> dba.plotVenn(ATAC_seq_Goett_peaks, consensus=DBA_TISSUE)
Error in dba.plotVenn(ATAC_seq_Goett_peaks, consensus = DBA_TISSUE) : 
  unused argument (consensus = DBA_TISSUE)
ADD REPLYlink written 11 days ago by theodore.georgomanolis0
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