HOMER mergepeaks matrix interpreatation

Question

[morovatunc]

Hi,

Has any one gotten experience on interpretting merge peaks matrix output.? I dont know what is the meaning of column and row names mean?

Thank you,

Best,

Tunc.

[Sukhi Singh]

Post the head here.

[morovatunc]

I will not bother with head :)

here is your information.

    peak overlap totals, cmd = mergePeaks -d 500 Helas3H2azPk.broadPeak.bed Helas3H3k04me1StdPk.broadPeak.bed Helas3H3k09me3Pk.broadPeak.bed Helas3H3k27acStdPk.broadPeak.bed Helas3H3k27me3StdPk.broadPeak.bed Helas3H3k36me3StdPk.broadPeak.bed Helas3H3k4me2StdPk.broadPeak.bed Helas3H3k4me3StdPk.broadPeak.bed Helas3H3k79me2StdPk.broadPeak.bed Helas3H3k9acStdPk.broadPeak.bed Helas3H4k20me1StdPk.broadPeak.bed -matrix hela    Helas3H2azPk.broadPeak.bed  Helas3H3k04me1StdPk.broadPeak.bed   Helas3H3k09me3Pk.broadPeak.bed  Helas3H3k27acStdPk.broadPeak.bed    Helas3H3k27me3StdPk.broadPeak.bed   Helas3H3k36me3StdPk.broadPeak.bed   Helas3H3k4me2StdPk.broadPeak.bed    Helas3H3k4me3StdPk.broadPeak.bed    Helas3H3k79me2StdPk.broadPeak.bed   Helas3H3k9acStdPk.broadPeak.bed Helas3H4k20me1StdPk.broadPeak.bed
Helas3H2azPk.broadPeak.bed  0   23545   4130    21410   1671    1087    28110   20670   4407    17885   8506
Helas3H3k04me1StdPk.broadPeak.bed   23508   0   2679    20489   896 2495    36955   15744   9951    11913   12935
Helas3H3k09me3Pk.broadPeak.bed  4303    2670    0   1392    1595    1376    2451    1409    3396    1320    8586
Helas3H3k27acStdPk.broadPeak.bed    20393   20244   1372    0   475 1128    26663   21911   3990    20355   4833
Helas3H3k27me3StdPk.broadPeak.bed   1666    886 1550    456 0   626 940 747 714 677 3013
Helas3H3k36me3StdPk.broadPeak.bed   1061    2454    1338    1110    630 0   1569    1080    3725    1159    4681
Helas3H3k4me2StdPk.broadPeak.bed    27390   36501   2417    27021   952 1594    0   27152   6528    19192   9420
Helas3H3k4me3StdPk.broadPeak.bed    19695   15511   1363    22050   747 1082    27056   0   4069    21611   4871
Helas3H3k79me2StdPk.broadPeak.bed   4626    10514   3551    4345    744 4011    7047    4392    0   4292    13898

[morovatunc]

I apologise for the formatting this is the best that I can provide. The rownames are supposed to be printed in the same order as colnames.

[Sukhi Singh]

Don't worry about the formatting, its clear. I will post an answer.

Answer 1

[Sukhi Singh]

So this matrix represents that how many peaks are shared between different file give by -d parameter. I don't understand why this matrix is produced, if you haven't mentioned -matrix parameter. But this file displays the raw count of overlapping peaks between several files.

Read about Peak Co-Occurrence Statistics

[morovatunc]

the mergePeaks itsefl works perfect. I understood it by heart. However, as you mention( sorry my bad I should have mentioned before), -matrix option created this intresting output. This is the reason why I asked the question.

So to be on the same page, should the matrix be symmetrical because say I have two files should the number of overlapping regions be same?

Similar to (A ∩ B) == (B∩A)

[Sukhi Singh]

Mathematically, the number of overlaps should be the same if the observations being overlapped are of the same size thus creating a symmetric matrix. But consider these tmp file A and B

A                         B 
peak1 1 1000      vs  peak 1 10 100
peak2 1500 2000      peak 2 110 200

Here, (A ∩ B) != (B ∩ A) as number of peaks in B overlapping first region in A=2 but vice versa=1.

That's why you could see some differences. If you are happy with the answer, you could mark it accepted. Good Luck!