Hi Khademul,

Regarding the speed concern with very big bed files, splitting the files chromosome by chromosome would help if you can run R in a cluster.

Regarding p-value for overlap, set totalTest appropriately is critical. Please refer to the posts.

http://permalink.gmane.org/gmane.science.biology.informatics.conductor/29476
http://permalink.gmane.org/gmane.science.biology.informatics.conductor/30115

Kind regards,

Julie


On 8/9/10 6:02 AM, "Khademul Islam" <khademul.islam@gmail.com> wrote:

Hi Julie,

Nice to see published ChIPpeakAnno paper.

I was trying to do overlapping between my ChIPseq peak bed file (peak1: ~3100 peaks) and Exon_Intron Boundary bed file ( peak2: ~400000 ).

There are two concerns:

1. Its takes too long time (overnight) to calculate all these even with powerful machine........., specially when one bed file is too big.

2. It produced "NaN" for p-value


$p.value
[1] NaN

$vennCounts
     peak1 peak2  Counts
[1,]     0     0 -398821
[2,]     0     1  395828
[3,]     1     0    2253
[4,]     1     1     840
attr(,"class")
[1] "VennCounts"


So it counts "-" (minus) -398821 ???

There were 22 warnings but no other error. Warning says that it produces "NaN"

I pasted warnings below. I wanted to attach the bed files if you need to check, but its too large. Well, in case if you need it, let me know, I will upload it in FTP site. I got the venn diagram pic without any problem (attached).

Command line was:


ol <- findOverlappingPeaks(peaks1, peaks2, maxgap=1, multiple=F, NameOfPeaks1="Peak1", NameOfPeaks2="Peak2")

vdg <- makeVennDiagram(RangedDataList(peaks1, peaks2), NameOfPeaks=c("peak1", "peak2"), maxgap=0, totalTest=100, cex = 1, counts.col = "red")

> dev.copy2eps()

> vdg


So, my question is, how can I get proper p-value from the overlap, what I have to do to fix it?

Thank you,

Khademul



> sessionInfo()
R version 2.11.1 (2010-05-31)
x86_64-unknown-linux-gnu

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
 [1] ChIPpeakAnno_1.4.1
.....

> warnings()
Warning messages:
1: In .local(query, subject, maxgap, minoverlap, type, select,  ... :
  argument 'multiple' is deprecated; use 'select'.
2: In .local(query, subject, maxgap, minoverlap, type, select,  ... :
  argument 'multiple' is deprecated; use 'select'.
3: In .local(query, subject, maxgap, minoverlap, type, select,  ... :
  argument 'multiple' is deprecated; use 'select'.
4: In .local(query, subject, maxgap, minoverlap, type, select,  ... :
  argument 'multiple' is deprecated; use 'select'.
5: In .local(query, subject, maxgap, minoverlap, type, select,  ... :
  argument 'multiple' is deprecated; use 'select'.
6: In .local(query, subject, maxgap, minoverlap, type, select,  ... :
  argument 'multiple' is deprecated; use 'select'.
7: In .local(query, subject, maxgap, minoverlap, type, select,  ... :
  argument 'multiple' is deprecated; use 'select'.
8: In .local(query, subject, maxgap, minoverlap, type, select,  ... :
  argument 'multiple' is deprecated; use 'select'.
9: In .local(query, subject, maxgap, minoverlap, type, select,  ... :
  argument 'multiple' is deprecated; use 'select'.
10: In .local(query, subject, maxgap, minoverlap, type, select,  ... :
  argument 'multiple' is deprecated; use 'select'.
11: In .local(query, subject, maxgap, minoverlap, type, select,  ... :
  argument 'multiple' is deprecated; use 'select'.
12: In .local(query, subject, maxgap, minoverlap, type, select,  ... :
  argument 'multiple' is deprecated; use 'select'.
13: In .local(query, subject, maxgap, minoverlap, type, select,  ... :
  argument 'multiple' is deprecated; use 'select'.
14: In .local(query, subject, maxgap, minoverlap, type, select,  ... :
  argument 'multiple' is deprecated; use 'select'.
15: In .local(query, subject, maxgap, minoverlap, type, select,  ... :
  argument 'multiple' is deprecated; use 'select'.
16: In .local(query, subject, maxgap, minoverlap, type, select,  ... :
  argument 'multiple' is deprecated; use 'select'.
17: In .local(query, subject, maxgap, minoverlap, type, select,  ... :
  argument 'multiple' is deprecated; use 'select'.
18: In .local(query, subject, maxgap, minoverlap, type, select,  ... :
  argument 'multiple' is deprecated; use 'select'.
19: In .local(query, subject, maxgap, minoverlap, type, select,  ... :
  argument 'multiple' is deprecated; use 'select'.
20: In .local(query, subject, maxgap, minoverlap, type, select,  ... :
  argument 'multiple' is deprecated; use 'select'.
21: In .local(query, subject, maxgap, minoverlap, type, select,  ... :
  argument 'multiple' is deprecated; use 'select'.
22: In phyper(q, m, n, k, lower.tail, log.p) : NaNs produced














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