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Question: DiffBind masks for counts
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gravatar for rbronste
12 weeks ago by
rbronste20
rbronste20 wrote:

Trying to generate replicate masks for the dba.count function from a .csv where I list 3 replicates under DBA_CONDITION. Want to do dba.counts with minMembers = 3 to include only those that are in all 3 of each replicate group for the binding matrix. Any clues on how to do this? Thanks.

ADD COMMENTlink modified 11 weeks ago by Rory Stark2.1k • written 12 weeks ago by rbronste20
1
gravatar for Rory Stark
11 weeks ago by
Rory Stark2.1k
CRUK, Cambridge, UK
Rory Stark2.1k wrote:

I'm not sure exactly what your sample sheet looks like for this. Do you have three replicates of each condition, where each replicated sample has the same DBA_CONDITION value, but a different replicate number? And you want to keep peaks for one specific value condition?

Is this the same project as in question #DiffBind contrasts issue And you would to, for example, use dba.count() to make a binding matrix with all the peaks that are in all three MALE/TREATMENT replicates? If that is what you want to do, this should work:

> masks <- CHIP_adult_BN_peaks$masks
> CHIP_adult_BN_mask_MaleTRE  <- masks$MALE & masks$TREATMENT
> CHIP_adult_BN_peaks_MaleTRE <- 
      dba(CHIP_adult_BN_peaks,mask=CHIP_adult_BN_mask_MaleTRE, 
          minMembers=3)
> CHIP_adult_BN_consensus_MaleTRE <- 
      dba(CHIP_adult_BN_peaks_MaleTRE, bRetrieve=TRUE)
> CHIP_adult_BN_counts <- dba.count(CHIP_adult_BN_peaks, 
                                    peaks=CHIP_adult_BN_consensus_MaleTRE)

 

ADD COMMENTlink modified 10 weeks ago • written 11 weeks ago by Rory Stark2.1k

Yes this is the same as the other thread, forgot to remove this one after posting. So yes basically have a sheet with male/female vehicle/treatment so 12 samples with 3 reps each (e.g. 3 replicates for Male Vehicle) and want the counts to only add to matrix if peaks in all 3 replicates for one group like Male Vehicle. Does that make sense?

ADD REPLYlink written 11 weeks ago by rbronste20
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