How to use DiffBind to get consensus peaks I am interested in?
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Gary ▴ 20
@gary-7967
Last seen 2.6 years ago

Hi,

I wound like to get 2,913 consensus peaks that in Early stage, but not in Late stage samples (fig1). They are overlapping between T8E_HMC & T9E_HMC samples, but not in T8L_HMC and T9L_HMC samples (fig1). I have tried the dba.peakset command, but doesn't work. Could you show me how to do it correctly? The best way is to get a .bed file for the downstream analysis. Below are commands I used to get this Venn diagram for your reference.  Thank you so much.

Best,

Gary

 

> t8t9=dba(sampleSheet = "t8t9.csv",peakFormat = "bed")

T8E_HMC MSC Early T8  1 MACS

T9E_HMC MSC Early T9  2 MACS

T8L_HMC MSC Late T8  1 MACS

T9L_HMC MSC Late T9  2 MACS

> t8t9

4 Samples, 15919 sites in matrix (39174 total):

       ID Tissue Factor Condition Replicate Caller Intervals

1 T8E_HMC    MSC  Early        T8         1   MACS     21905

2 T9E_HMC    MSC  Early        T9         2   MACS     23327

3 T8L_HMC    MSC   Late        T8         1   MACS     12377

4 T9L_HMC    MSC   Late        T9         2   MACS     12902

> names(t8t9$masks)

 [1] "MSC"         "Early"       "Late"        "T8"          "T9"          ""            "MACS"        "Replicate.1" "Replicate.2" "All"        

[11] "None"      

> dba.plotVenn(t8t9,t8t9$masks$MSC)

 

fig1

fig1

DiffBind • 1.4k views
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Rory Stark ★ 4.1k
@rory-stark-5741
Last seen 14 days ago
CRUK, Cambridge, UK

Hi Gary-

You can use dba.overlap() as follows:

> t8t9.overlaps <- dba.overlap(t8t9,t8t9$masks$MSC)

t8t9.overlaps will contain the peaksets for all 15 positions in the Venn diagram:

> names(t8t9.overlaps)

The one you want will be called t8t9.overlaps$AandB:

> t8t9.overlaps$AandB

This is a GRanges object by default (you can get them back as a dataframe by setting DataType=DBA_DATA_FRAME).

You can also get the same data back from the call to dba.plotVenn() by setting bReturnPeaksets=TRUE (in the development version moving forward, these are returned "invisibly" and the bReturnPeaksets parameter has been eliminated).

Cheers-

Rory

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Hi Rory,

Thank you so much. I have tried what you suggested, but I don't know how to save the result as a txt file. I know it's not a DiffBind question, but could you help me again? Many thanks. Below are command lines I used for your reference.

Best,

Gary

 

> t8t9=dba(sampleSheet = "t8t9.csv",peakFormat = "bed")
T8E_HMC MSC Early T8  1 MACS
T9E_HMC MSC Early T9  2 MACS
T8L_HMC MSC Late T8  1 MACS
T9L_HMC MSC Late T9  2 MACS
> t8t9
4 Samples, 15919 sites in matrix (39174 total):
       ID Tissue Factor Condition Replicate Caller Intervals
1 T8E_HMC    MSC  Early        T8         1   MACS     21905
2 T9E_HMC    MSC  Early        T9         2   MACS     23327
3 T8L_HMC    MSC   Late        T8         1   MACS     12377
4 T9L_HMC    MSC   Late        T9         2   MACS     12902
> names(t8t9$masks)
 [1] "MSC"         "Early"       "Late"        "T8"          "T9"          ""           
 [7] "MACS"        "Replicate.1" "Replicate.2" "All"         "None"       
> dba.plotVenn(t8t9, t8t9$masks$MSC)
> t8t9.overlaps <-dba.overlap(t8t9,t8t9$masks$MSC)
> names(t8t9.overlaps)
 [1] "onlyA" "onlyB" "onlyC" "onlyD" "AandB" "AandC" "AandD" "BandC" "BandD" "CandD" "notA" 
[12] "notB"  "notC"  "notD"  "inAll"
> t8t9.overlaps$AandB
GRanges object with 2913 ranges and 2 metadata columns:
        seqnames               ranges strand   |             scoreA             scoreB
           <Rle>            <IRanges>  <Rle>   |          <numeric>          <numeric>
     24     chr1   [ 564352,  570445]      *   |  0.046839174582378 0.0234009360374415
     55     chr1   [ 900161,  901002]      *   | 0.0167048804454635 0.0227769110764431
     71     chr1   [1009781, 1010682]      *   | 0.0347199475925319 0.0277691107644306
     77     chr1   [1047306, 1048373]      *   | 0.0252210940058958 0.0162246489859594
     94     chr1   [1218174, 1218917]      *   | 0.0212905339010809 0.0287051482059282
    ...      ...                  ...    ... ...                ...                ...
  39020     chrY [ 2427812,  2428479]      *   | 0.0370127743203406 0.0271450858034321
  39091     chrY [10018797, 10020074]      *   | 0.0216180805764821 0.0168486739469579
  39125     chrY [13671130, 13672096]      *   | 0.0458565345561743 0.0215288611544462
  39127     chrY [13682255, 13683846]      *   | 0.0255486406812971 0.0290171606864275
  39137     chrY [13816319, 13823737]      *   | 0.0674746151326564 0.0464898595943838
  -------
  seqinfo: 33 sequences from an unspecified genome; no seqlengths
> write.table(t8t9.overlaps$AandB,"./t8t9.overlapsAandB.txt")
Error in as.vector(x) : no method for coercing this S4 class to a vector
> write.table(t8t9.overlaps$AandB,file="t8t9overlapsAandB.txt")
Error in as.vector(x) : no method for coercing this S4 class to a vector

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Thanks a lot.

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Thanks a lot.

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