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
>>
>>
>
>
