JASPAR annotation

[rojinsafavi]

Hi @rcorces
When I use JASPAR motif annotation, the addMotifAnnotations gives 633 TFs. I checked JASPAR database and there are around 1200 Homosapien TF. I was wondering if there is a specific reason that the number is much lower?

[rcorces]

ArchR uses bioconductor packages to obtain motif sets. For example, JASPAR2020.

ArchR/R/AnnotationPeaks.R

Lines 330 to 337 in 968e442

	if(tolower(motifSet)=="jaspar2020"){
	.requirePackage("JASPAR2020",installInfo='BiocManager::install("JASPAR2020")')
	args <- list(species = species, collection = collection, ...)
	motifs <- TFBSTools::getMatrixSet(JASPAR2020::JASPAR2020, args)
	obj <- .summarizeJASPARMotifs(motifs)
	motifs <- obj$motifs
	motifSummary <- obj$motifSummary

I'm not sure about the exact numbers but ArchR doesnt modify these motif sets. I'd recommend following up with the maintainers of those packages to understand any discrepancies.

> ArchR:::.requirePackage("JASPAR2020",installInfo='BiocManager::install("JASPAR2020")')
> args <- list(species = "Homo sapiens", collection = "CORE")
> motifs <- TFBSTools::getMatrixSet(JASPAR2020::JASPAR2020, args)
> motifs
PFMatrixList of length 633 names(633): MA0030.1 MA0031.1 MA0051.1 MA0057.1 MA0059.1 MA0066.1 MA0069.1 MA0070.1 ... MA0814.2 MA1123.2 MA0093.3 MA0526.3 MA0748.2 MA0528.2 MA0609.2

[rojinsafavi]

@rcorces I looked at TFBTools, I think the reason the number is lower is that not all versions are used.

this piece of code will give 810 TF

args <- list(species = "Homo sapiens", collection = "CORE", all_versions = TRUE)
motifs <- TFBSTools::getMatrixSet(JASPAR2020::JASPAR2020, args)
PFMatrixList of length 810
names(810): MA0002.1 MA0003.1 MA0017.1 MA0018.1 ... MA0748.2 MA0528.2 MA0609.2

Is there a straightforward way to add this argument to ArchR?

[rcorces]

yes - if you look at the function documentation, you will see that we provide pass-through arguments to TFBSTools::getMatrixSet.

see ... at the bottom of https://www.archrproject.com/reference/addMotifAnnotations.html

So you just add whatever additional params you want to send to getMatrixSet() into the params you pass to addMotifAnnotations().

We allow pass-through arguments in most cases where ArchR calls another package's function (for ex. plotting functions that call ggPlot) but users seem to always miss this part of the documentation.

[rojinsafavi]

Thanks Ryan!

[LornaWessels]

Hi everyone,
related to this I tried filtering the JASPAR2020 TF motif set by those included in the TF collection from Lambert et al. 2018 (to remove complexes etc.)

The TFBSTools::getMatrixSet() function has the argument "name" which I can use to filter by the names of the TFs.
However, this is not possible with addMotifAnnotations() since the argument "name" is already used by ArchR for the name of the stored annotation.

I could still work around by passing a custom PWMatrixList though.
But it would be super nice if this filtering option would work in addMotifAnnotation() directly.

Best,
Lorna

[rcorces]

@LornaWessels - I could make this change. Could you open up a new issue to track this?

[sylestiel]

@rcorces

Can you help me figure out how to use the JASPAR2020 for addMotifAnnotations(). I tried the following and got an error.

args <- list(collection = "CORE", all_versions = TRUE)
motifL <- TFBSTools::getMatrixSet(JASPAR2020::JASPAR2020, args)
projC5.1 <- addMotifAnnotations(ArchRProj = projC5.1, motifSet ="JASPAR2020", name = "Motif",annoName = "motifL", force = TRUE)
ArchR-addMotifAnnotations-ef322eebf59e-Date-2022-07-11_Time-17-41-20.log

[rcorces]

@sylestiel - this is not the correct use of the function and its hard to know what you are trying to accomplish. See the function params.

ArchR/R/AnnotationPeaks.R

Lines 273 to 293 in f6c0388

	#' @param ArchRProj An `ArchRProject` object.
	#' @param motifSet The motif set to be used for annotation. Options include: (i) "JASPAR2016", "JASPAR2018", "JASPAR2020"
	#' which gives the 2016, 2018 or 2020 version of JASPAR motifs, (ii) one of "cisbp", "encode", or "homer" which gives the
	#' corresponding motif sets from the `chromVAR` package, or (iii) "vierstra" which gives the clustered archetype motifs
	#' created by Jeff Vierstra (https://github.com/jvierstra/motif-clustering).
	#' @param annoName The name of the `peakAnnotation` object to be stored in the provided `ArchRProject`
	#' @param species The name of the species relevant to the supplied `ArchRProject`. This is used for identifying which motif to be
	#' used from CisBP/JASPAR. By default, this function will attempt to guess the species based on the value from `getGenome()`.
	#' @param collection If one of the JASPAR motif sets is used via `motifSet`, this parameter allows you to indicate the JASPAR
	#' collection to be used. See `getMatrixSet()` from `TFBSTools` for all options to supply for collection. If `motifSet` is
	#' "vierstra", then this must either be "archetype" (for the v2.1 clustered models) or "individual" (for the original v1 individual motif models).
	#' NOTE: vierstra archetype motifs are currently in beta and have not been finalized by Jeff Vierstra.
	#' @param motifPWMs A custom set of motif PWMs as a PWMList for adding motif annotations.
	#' @param cutOff The p-value cutoff to be used for motif search. The p-value is determined vs a background set of sequences
	#' (see `MOODS` for more details on this determination).
	#' @param width The width in basepairs to consider for motif matches. See the `motimatchr` package for more information.
	#' @param version An integer specifying version 1 or version 2 of chromVARmotifs see github for more info GreenleafLab/chromVARmotifs.
	#' @param force A boolean value indicating whether to force the `peakAnnotation` object indicated by `annoName` to be overwritten if
	#' it already exists in the given `ArchRProject`.
	#' @param logFile The path to a file to be used for logging ArchR output.
	#' @param ... Additional parameters to be passed to `TFBSTools::getMatrixSet` for getting a JASPAR PWM object.

you do not need to call TFBSTools prior to addMotifAnnotations. Also, your log file does not include your error. The param name in your code is being passed to TFBSTools::getMatrixSet.

[sylestiel]

Thanks!