Hi Dr. Rory Stark,

      I used your "DiffBind" to analysis Chip-seq data by following codes. However, I could not get the table which used to plot heatmap (different binding sites? What is the threshold?). Could you give me some advice? Thanks very much.

Codes:

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setwd("/data/fmao/rajesh/hMeDIP/DiffBind")

pdf("draw.DiffBind.final.pdf")

hmedip <- dba(sampleSheet="config.csv")

plot(hmedip,main="using occupancy (peak caller score) data")

hmedip <- dba.count(hmedip)

hmedip1 <- dba.contrast(hmedip, categories=DBA_CONDITION,minMembers=2)

hmedip2 <- dba.analyze(hmedip1)

dba.plotHeatmap(hmedip2, contrast=1, correlations=FALSE,main="Contrast Heatmap")

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dba.plotHeatmap() returns the underlying matrix it plotted "invisibly", so if you assign it to a variable, you can see it. For a read score heatmap (correlations=FALSE), this is returned as a GRanges object with all the selected sites and their read scores, in the order they appear as rows in the plot.

For example:

> data(tamoxifen_analysis)
> DBsites <- dba.plotHeatmap(tamoxifen,contrast=1,correlations=FALSE)
> granges(DBsites)
GRanges object with 677 ranges and 0 metadata columns:
       seqnames               ranges strand
          <Rle>            <IRanges>  <Rle>
   106    chr18 [ 2534348,  2534848]      *
  2272    chr18 [59589912, 59590412]      *
   897    chr18 [24348927, 24349427]      *
   107    chr18 [ 2537580,  2538080]      *
  1986    chr18 [53069041, 53069541]      *
   ...      ...                  ...    ...
  2641    chr18 [71562750, 71563250]      *
  2243    chr18 [59256493, 59256993]      *
  1645    chr18 [43620150, 43620650]      *
  1186    chr18 [32306249, 32306749]      *
  1759    chr18 [46474665, 46475165]      *
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths

Remember that by default, at most 1,000 sites will be used (starting with site having the lowest FDR) -- you can change this with the maxSites parameter.