different TSS.filter values affect the signals showing on the heatmap

[hyjforesight]

Hello @jianhong Thanks for pushing the patch fixing the NA problem. I can generate the complete heatmap now. However, the red signals of heatmap are still partially shown on the yellow background.

NTILE <- 101
dws <- ups <- 1010
sigs <- enrichedFragments(gal=objs[c("NucleosomeFree", "mononucleosome", "dinucleosome", "trinucleosome")], TSS=TSS, librarySize=librarySize, upstream = ups, downstream = dws, TSS.filter=0.5, seqlev = paste0("chr", c(1:19, "X", "Y")), n.tile = NTILE)
sigs.log2 <- lapply(sigs, function(.ele) log2(.ele+1))
ATACheatmap <- featureAlignedHeatmap(cvglists=sigs.log2, feature.gr=reCenterPeaks(peaks=TSS, width=ups+dws), upstream = ups, downstream = dws, zeroAt=0.5, n.tile=NTILE)

I found the area of red signals showing on the heatmap depends on the value of TSS.filter in sigs <- enrichedFragments(). I tried several different values of TSS.filter, but whatever the value is, I still cannot get the complete heatmap. Here is an example for TSS.filter=10. The area of red signal becomes bigger, but still not completed.

sigs <- enrichedFragments(gal=objs[c("NucleosomeFree", "mononucleosome", "dinucleosome", "trinucleosome")], TSS=TSS, librarySize=librarySize, upstream = ups, downstream = dws, TSS.filter=10, seqlev = paste0("chr", c(1:19, "X", "Y")), n.tile = NTILE)
sigs.log2 <- lapply(sigs, function(.ele) log2(.ele+1))
ATACheatmap <- featureAlignedHeatmap(cvglists=sigs.log2, feature.gr=reCenterPeaks(peaks=TSS, width=ups+dws), upstream = ups, downstream = dws, zeroAt=0.5, n.tile=NTILE)

Here also attached my TSS score plot.

Appreciate it if you could give me some recommendations about how to determine the best TSS.filter for generating the complete heatmap! Thanks! Best, YJ

[jianhong]

@hyjforesight Sorry for the late replay. I missed this email. Could you please share the minimized bam file to repeat your issue?