Question: DiffBind masks for counts
gravatar for rbronste
13 months ago by
rbronste60 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 13 months ago by Rory Stark2.5k • written 13 months ago by rbronste60
gravatar for Rory Stark
13 months ago by
Rory Stark2.5k
CRUK, Cambridge, UK
Rory Stark2.5k 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 <- 
> CHIP_adult_BN_consensus_MaleTRE <- 
      dba(CHIP_adult_BN_peaks_MaleTRE, bRetrieve=TRUE)
> CHIP_adult_BN_counts <- dba.count(CHIP_adult_BN_peaks, 


ADD COMMENTlink modified 13 months ago • written 13 months ago by Rory Stark2.5k

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 13 months ago by rbronste60
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 225 users visited in the last hour