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Question: DiffBind Question
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5.2 years ago by
Rory Stark2.6k
CRUK, Cambridge, UK
Rory Stark2.6k wrote:
Hi Stephen- 1. dba.analyze itself doesn't use any thresholds, it just computes the p-values and FDRs for every binding site. The thresholds are used in the reporting and plotting functions: dba.report, dba.plotMA, dba.plotHeatmap, dba.plotPCA, and dba.plotBox. The generic plot function corresponds to dba.plotHeatmap and you can specify thresholds. eg: > DBSites = dba.report(DBA,contrast=1, th=.05, bUsePval=TRUE) > dba.plotMA(DBA, th=.05, bUsePvals=TRUE) NOTE: I've just added the ability to set the default threshold for the object instead of the global FDR < 0.1 currently implemented. This feature will appear in the development version (as 1.9.2) soon. These values will initialized as: > DBA$config$th = 0.1 > DBA$config$pUsePval = FALSE and can subsequently be changed at will. 2. You can export the entire affinity binding matrix (based on the consensus set after running dba.count) using dba.peakset. If you set the "bRetrieve" parameter to TRUE, this will return the entire matrix (the "DataType" parameter controls the form of how this is returned; default type is GRanges). If you set the "writeFile" parameter to a filename, the data will be exported to a tab-delimited file of that name. eg: > affinities = dba.peakset(DBA,writeFile="BindingAffintyMatrix.bed") Cheers- Rory On 17/10/2013 16:55, "Stephen Mack" <stephen.mack at="" mail.utoronto.ca=""> wrote: >Hi Rory, > >I was hoping you could help with with two DiffBind questions: > >1) Is it possible to adjust the p-value / FDR threshold for the >dba.analyze function ? > >2) Is it possible to export the consensus / affinity binding matrices ? > >Thanks, > >Stephen Mack > >Grad Student >The Hospital for Sick Children >Brain Tumour Research Centre >Toronto, ON >Canada
modified 5.2 years ago • written 5.2 years ago by Rory Stark2.6k
0
5.2 years ago by
Rory Stark2.6k
CRUK, Cambridge, UK
Rory Stark2.6k wrote:
Hmmn, how exactly are you retrieving the matrix? When I run dba.peakset as described below, the columns are named using the DBA_ID value for the sample. Can you send a sessionInfo() so I can see what version you are working on? Here's what I see: > data(tamoxifen_counts) > tamoxifen = dba.count(tamoxifen,peaks=NULL,score=DBA_SCORE_READS) > dba.peakset(tamoxifen,bRetrieve=T) GRanges with 1654 ranges and 11 metadata columns: seqnames ranges strand | BT474.1. BT474.2. MCF7.1. MCF7.2. MCF7.3. T47D.1. T47D.2. MCF7.1..1 MCF7.2..1 ZR75.1. ZR75.2. <rle> <iranges> <rle> | <numeric> <numeric> <numeric> <numeric> <numeric> <numeric> <numeric> <numeric> <numeric> <numeric> <numeric> 1 chr18 [ 95744, 102011] * | 2494 2239 2885 2202 2624 2951 7185 2125 1532 6399 13055 2 chr18 [179080, 179752] * | 16 25 28 20 46 4 10 77 64 19 53 3 chr18 [205229, 206269] * | 32 69 11 15 33 9 44 20 26 119 208 4 chr18 [301531, 302260] * | 52 40 21 14 9 6 19 3 9 34 78 5 chr18 [336592, 337347] * | 19 13 71 38 48 6 37 11 15 15 27 ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 1650 chr18 [75641971, 75642647] * | 3 7 39 25 41 17 16 8 5 13 40 1651 chr18 [75795125, 75796156] * | 53 60 204 84 152 15 26 57 21 14 22 1652 chr18 [75826088, 75826939] * | 36 45 23 14 33 25 36 40 22 46 80 1653 chr18 [76068994, 76069874] * | 64 64 58 44 58 9 42 90 52 51 155 1654 chr18 [76087923, 76089259] * | 27 10 74 50 58 11 32 43 26 232 603 --- seqlengths: chr18 NA Where "BT424.1." is a sample name. It turns out that GRanges doesn't like the "+" and "-" -- you can see them if you get the result back as a data.frame: > head(dba.peakset(tamoxifen,bRetrieve=T,DataType=DBA_DATA_FRAME)) CHR START END BT474.1- BT474.2- MCF7.1+ MCF7.2+ MCF7.3+ T47D.1+ T47D.2+ MCF7.1- MCF7.2- ZR75.1+ ZR75.2+ 1 chr18 95744 102011 2494 2239 2885 2202 2624 2951 7185 2125 1532 6399 13055 2 chr18 179080 179752 16 25 28 20 46 4 10 77 64 19 53 3 chr18 205229 206269 32 69 11 15 33 9 44 20 26 119 208 4 chr18 301531 302260 52 40 21 14 9 6 19 3 9 34 78 5 chr18 336592 337347 19 13 71 38 48 6 37 11 15 15 27 6 chr18 346557 347362 53 52 11 13 13 9 25 12 13 23 51 Cheers- Rory On 17/10/2013 21:15, "Stephen Mack" <stephen.mack at="" mail.utoronto.ca=""> wrote: >Thanks Rory, > >When the matrix is exported, it looks like it's without headers >indicating sample IDs. Is there any way of exporting these or determining >what the order is? I assume it's just the same order that the samples >were read in from left to right? > >Cheers, > >Steve > > >On 2013-10-17, at 12:49 PM, Rory Stark <rory.stark at="" cruk.cam.ac.uk=""> wrote: > >> Hi Stephen- >> >> 1. dba.analyze itself doesn't use any thresholds, it just computes the >> p-values and FDRs for every binding site. The thresholds are used in the >> reporting and plotting functions: dba.report, dba.plotMA, >>dba.plotHeatmap, >> dba.plotPCA, and dba.plotBox. The generic plot function corresponds to >> dba.plotHeatmap and you can specify thresholds. eg: >> >>> DBSites = dba.report(DBA,contrast=1, th=.05, bUsePval=TRUE) >>> dba.plotMA(DBA, th=.05, bUsePvals=TRUE) >> >> NOTE: I've just added the ability to set the default threshold for the >> object instead of the global FDR < 0.1 currently implemented. This >>feature >> will appear in the development version (as 1.9.2) soon. These values >>will >> initialized as: >> >>> DBA$config$th = 0.1 >>> DBA$config$pUsePval = FALSE >> >> and can subsequently be changed at will. >> >> 2. You can export the entire affinity binding matrix (based on the >> consensus set after running dba.count) using dba.peakset. If you set the >> "bRetrieve" parameter to TRUE, this will return the entire matrix (the >> "DataType" parameter controls the form of how this is returned; default >> type is GRanges). If you set the "writeFile" parameter to a filename, >>the >> data will be exported to a tab-delimited file of that name. eg: >> >>> affinities = dba.peakset(DBA,writeFile="BindingAffintyMatrix.bed") >> >> Cheers- >> Rory >> >> >> On 17/10/2013 16:55, "Stephen Mack" <stephen.mack at="" mail.utoronto.ca=""> >>wrote: >> >>> Hi Rory, >>> >>> I was hoping you could help with with two DiffBind questions: >>> >>> 1) Is it possible to adjust the p-value / FDR threshold for the >>> dba.analyze function ? >>> >>> 2) Is it possible to export the consensus / affinity binding matrices ? >>> >>> Thanks, >>> >>> Stephen Mack >>> >>> Grad Student >>> The Hospital for Sick Children >>> Brain Tumour Research Centre >>> Toronto, ON >>> Canada >> >> > >