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Showing content from https://github.com/stuart-lab/signac/issues/1098 below:

Reopening Overlay TF footprints for different feature sets (#1080) · Issue #1098 · stuart-lab/signac · GitHub

Hi,

I'm reopening this because I wasn't successful in trying to implement your suggestion.

On a single footprint plot, I am aiming to overlay:
footprint around motif X from cells Y computed from peakset.1,
footprint around motif X from cells Y computed from peakset.2,

instances.1 <- matchMotifs(pwm, StringToGRanges(peakset.1), genome = "mm10", out='positions')
instances.2 <- matchMotifs(pwm, StringToGRanges(peakset.2), genome = "mm10", out='positions')

integrated <- Footprint(
  object =integrated,
  key=clst,
  assay='mac.peaks',
  genome = BSgenome.Mmusculus.UCSC.mm10,
  regions=c(instances.1, instances.2)
)

Running the above gives:

| | 0 % ~calculating Error in as.vector(x, mode) :
coercing an AtomicList object to an atomic vector is supported only for
objects with top-level elements of length <= 1
In addition: Warning message:
In if (any(strand(x = x) == "*")) { :
the condition has length > 1 and only the first element will be used

Running instances.1 without instances.2 gives the same error.

Would you be able to suggest a workaround? I can provide more code if needed.

Thanks.


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