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AnnotationPeaks.R
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##########################################################################################
# Annotation Methods
##########################################################################################
#' Get peakAnnotation from an ArchRProject
#'
#' This function gets a peakAnnotation from a given ArchRProject.
#'
#' @param ArchRProj An `ArchRProject` object.
#' @param name The name of the `peakAnnotation` object (i.e. Motifs) to retrieve from the designated `ArchRProject`.
#' @export
getPeakAnnotation <- function(ArchRProj = NULL, name = NULL){
.validInput(input = ArchRProj, name = "ArchRProj", valid = c("ArchRProj"))
.validInput(input = name, name = "name", valid = c("character", "null"))
if(is.null(name)){
name <- 1
}else{
if(name %ni% names(ArchRProj@peakAnnotation)){
stop("Name is not in peakAnnotation!")
}
}
ArchRProj@peakAnnotation[[name]]
}
#' Get peak annotation positions from an ArchRProject
#'
#' This function gets the peak annotation positions (i.e. Motifs) from a given ArchRProject.
#'
#' @param ArchRProj An `ArchRProject` object.
#' @param name The name of the `peakAnnotation` object (i.e. Motifs) to retrieve from the designated `ArchRProject`.
#' @param annoName The name of a specific annotation to subset within the `peakAnnotation`.
#' @export
getPositions <- function(ArchRProj = NULL, name = NULL, annoName = NULL){
.validInput(input = ArchRProj, name = "ArchRProj", valid = c("ArchRProj"))
.validInput(input = name, name = "name", valid = c("character", "null"))
.validInput(input = annoName, name = "annoName", valid = c("character", "null"))
if(is.null(name)){
name <- 1
}else{
if(name %ni% names(ArchRProj@peakAnnotation)){
stop("Name is not in peakAnnotation!")
}
}
anno <- ArchRProj@peakAnnotation[[name]]
idx <- grep("positions", names(anno), ignore.case=TRUE)
if(length(idx)==0){
stop("peakAnnotation does not contain positions!")
}
positions <- readRDS(anno[[idx]])
if(!is.null(annoName)){
idx <- grep(annoName, names(positions), ignore.case=TRUE)
if(length(idx)==0){
stop("Positons do not contain annoName!")
}
positions <- positions[idx]
}
positions
}
#' Get peak annotation matches from an ArchRProject
#'
#' This function gets peak annotation matches from a given ArchRProject. The peaks in the returned object are in the
#' same order as the peaks returned by `getPeakSet()`.
#'
#' @param ArchRProj An `ArchRProject` object.
#' @param name The name of the `peakAnnotation` object (i.e. Motifs) to retrieve from the designated `ArchRProject`.
#' @param annoName The name of a specific annotation to subset within the `peakAnnotation`.
#' @export
getMatches <- function(ArchRProj = NULL, name = NULL, annoName = NULL){
.validInput(input = ArchRProj, name = "ArchRProj", valid = c("ArchRProj"))
.validInput(input = name, name = "name", valid = c("character", "null"))
.validInput(input = annoName, name = "annoName", valid = c("character", "null"))
if(is.null(name)){
name <- 1
}else{
if(name %ni% names(ArchRProj@peakAnnotation)){
stop("Name is not in peakAnnotation!")
}
}
anno <- ArchRProj@peakAnnotation[[name]]
idx <- grep("matches", names(anno), ignore.case=TRUE)
if(length(idx)==0){
stop("peakAnnotation does not contain positions!")
}
matches <- readRDS(anno[[idx]])
if(!is.null(annoName)){
idx <- grep(annoName, colnames(matches), ignore.case=TRUE)
if(length(idx)==0){
stop("Matches do not contain annoName!")
}
matches <- matches[, idx, drop=FALSE]
}
matches
}
#' Add peak annotations to an ArchRProject
#'
#' This function adds information about which peaks contain input regions to a given ArchRProject. For each peak, a
#' binary value is stored indicating whether each region is observed within the peak region.
#'
#' @param ArchRProj An `ArchRProject` object.
#' @param regions A named `list` of `GRanges` that are to be overlapped with the `peakSet` in the `ArchRProject`.
#' @param name The name of `peakAnnotation` object to be stored as in `ArchRProject`.
#' @param force A boolean value indicating whether to force the `peakAnnotation` object indicated by `name` 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.
#' @export
addPeakAnnotations <- function(
ArchRProj = NULL,
regions = NULL,
name = "Region",
force = FALSE,
logFile = createLogFile("addPeakAnnotations")
){
.validInput(input = ArchRProj, name = "ArchRProj", valid = c("ArchRProj"))
.validInput(input = regions, name = "regions", valid = c("grangeslist", "character"))
.validInput(input = name, name = "name", valid = c("character"))
.validInput(input = force, name = "force", valid = c("boolean"))
.validInput(input = logFile, name = "logFile", valid = c("character"))
tstart <- Sys.time()
.startLogging(logFile = logFile)
.logThis(mget(names(formals()),sys.frame(sys.nframe())), "addPeakAnnotations Input-Parameters", logFile = logFile)
if(name %in% names(ArchRProj@peakAnnotation)){
if(force){
.logMessage("peakAnnotation name already exists! Overriding.", verbose = TRUE, logFile = logFile)
}else{
.logStop("peakAnnotation name already exists! set force = TRUE to override!", logFile = logFile)
}
}
if(inherits(regions, "GRanges")){
regionPositions <- GRangesList(region = regions)
}else{
if(is.null(names(regions))){
names(regions) <- paste0("Region_", seq_along(regions))
}
if(any(duplicated(names(regions)))){
stop("Found duplicated region names! Please make unique!")
}
regionPositions <- lapply(seq_along(regions), function(x){
.logThis(regions[[x]], paste0("regions[[x]]-", x), logFile = logFile)
if(inherits(regions[[x]], "GRanges")){
gr <- .validGRanges(regions[[x]])
}else if(is.character(regions[[x]])){
gr <- tryCatch({
makeGRangesFromDataFrame(
df = data.frame(data.table::fread(regions[[x]])),
keep.extra.columns = FALSE,
seqnames.field = "V1",
start.field = "V2",
end.field = "V3"
)
}, error = function(y){
.logMessage(paste0("Could not successfully get region : ", regions[[x]]), verbose = TRUE, logFile = logFile)
if(!file.exists(regions[[x]])){
.logStop(paste0("If region provided is a path it does not exist!"), logFile = logFile)
}
.logStop("Could not create GRanges from region", logFile = logFile)
})
}else{
.logStop("Unrecognized input in regions please input GRanges, GRangesList, or Paths to bed files!", logFile = logFile)
}
gr
}) %>% GRangesList
names(regionPositions) <- names(regions)
}
#############################################################
# Peak Overlap Matrix
#############################################################
peakSet <- getPeakSet(ArchRProj)
if(is.null(peakSet)){
.logStop("peakSet is NULL. You need a peakset to run addMotifAnnotations! See addReproduciblePeakSet!", logFile = logFile)
}
allPositions <- unlist(regionPositions, use.names=TRUE)
.logDiffTime("Creating Peak Overlap Matrix", t1 = tstart, verbose = TRUE, logFile = logFile)
overlapRegions <- findOverlaps(peakSet, allPositions, ignore.strand=TRUE)
if(length(overlapRegions) == 0){
stop("No Overlaps Found between regions and peak Matrix!")
}
.logThis(overlapRegions, "overlapRegions", logFile = logFile)
regionMat <- Matrix::sparseMatrix(
i = queryHits(overlapRegions),
j = match(names(allPositions),names(regionPositions))[subjectHits(overlapRegions)],
x = rep(TRUE, length(overlapRegions)),
dims = c(length(peakSet), length(regionPositions))
)
colnames(regionMat) <- names(regionPositions)
.logThis(regionMat, "regionMat", logFile = logFile)
regionMat <- SummarizedExperiment::SummarizedExperiment(assays=SimpleList(matches = regionMat), rowRanges = peakSet)
.logThis(regionMat, "regionSE", logFile = logFile)
#############################################################
# Filter Regions With No Matches
#############################################################
#Number of Overlaps
nO <- Matrix::colSums(assay(regionMat))
rF <- names(which(nO == 0))
if(all(nO == 0)){
stop("No Overlaps Found! Please check your peakSet and genome!")
}
if(length(rF) > 0){
.logDiffTime(paste0("Filtering Region Annotations with 0 overlaps :\n\n ", paste(rF, collapse=", "), "\n\n"), t1 = tstart, verbose = TRUE, logFile = logFile)
#Filter
regionPositions <- regionPositions[!(names(regionPositions) %in% rF)]
regionMat <- regionMat[,names(regionPositions),drop=FALSE]
}else{
.logDiffTime(paste0("All Regions Overlap at least 1 peak!"), t1 = tstart, verbose = TRUE, logFile = logFile)
}
#############################################################
# Summarize and Save
#############################################################
dir.create(file.path(getOutputDirectory(ArchRProj), "Annotations"), showWarnings=FALSE)
savePositions <- file.path(getOutputDirectory(ArchRProj), "Annotations", paste0(name,"-Positions-In-Peaks.rds"))
saveMatches <- file.path(getOutputDirectory(ArchRProj), "Annotations", paste0(name,"-Matches-In-Peaks.rds"))
out <- SimpleList(
regionMatches = regionMat,
regionPositions = regionPositions,
date = Sys.Date()
)
ArchRProj@peakAnnotation[[name]]$Name <- name
ArchRProj@peakAnnotation[[name]]$Positions <- savePositions
ArchRProj@peakAnnotation[[name]]$Matches <- saveMatches
.safeSaveRDS(out, file.path(getOutputDirectory(ArchRProj), "Annotations", paste0(name,"-In-Peaks-Summary.rds")), compress = FALSE)
.safeSaveRDS(out$regionPositions, savePositions, compress = FALSE)
.safeSaveRDS(out$regionMatches, saveMatches, compress = FALSE)
return(ArchRProj)
}
#' Add motif annotations to an ArchRProject
#'
#' This function adds information about which peaks contain motifs to a given ArchRProject. For each peak, a binary value
#' is stored indicating whether each motif is observed within the peak region.
#'
#' @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.
#' @export
addMotifAnnotations <- function(
ArchRProj = NULL,
motifSet = "cisbp",
annoName = "Motif",
species = NULL,
collection = "CORE",
motifPWMs = NULL,
cutOff = 5e-05,
width = 7,
version = 2,
force = FALSE,
logFile = createLogFile("addMotifAnnotations"),
...
){
.validInput(input = ArchRProj, name = "ArchRProj", valid = c("ArchRProj"))
.validInput(input = motifSet, name = "motifSet", valid = c("character", "null"))
.validInput(input = annoName, name = "annoName", valid = c("character"))
.validInput(input = species, name = "species", valid = c("character", "null"))
.validInput(input = collection, name = "collection", valid = c("character", "null"))
.validInput(input = cutOff, name = "cutOff", valid = c("numeric"))
.validInput(input = width, name = "width", valid = c("integer"))
.validInput(input = force, name = "force", valid = c("boolean"))
.validInput(input = logFile, name = "logFile", valid = c("character"))
if(!is.null(motifPWMs)){
if(!is(motifPWMs, "PWMatrixList")){
stop("User Supplied motifPWMS must be a PWMatrixList!")
}
motifSet <- "Custom"
}
if(is.null(motifSet)){
stop("Must provide motifSet or motifPWMs!")
}
.requirePackage("motifmatchr", installInfo='BiocManager::install("motifmatchr")')
tstart <- Sys.time()
.startLogging(logFile = logFile)
.logThis(mget(names(formals()),sys.frame(sys.nframe())), "addMotifAnnotations Input-Parameters", logFile = logFile)
if(annoName %in% names(ArchRProj@peakAnnotation)){
if(force){
message("peakAnnotation name already exists! Overriding.")
}else{
stop("peakAnnotation name already exists! set force = TRUE to override!")
}
}
if(grepl("JASPAR|CISBP", motifSet, ignore.case = TRUE) & is.null(species)){
if(grepl("hg19",getGenomeAnnotation(ArchRProj)$genome, ignore.case = TRUE)){
species <- "Homo sapiens"
}
if(grepl("hg38",getGenomeAnnotation(ArchRProj)$genome, ignore.case = TRUE)){
species <- "Homo sapiens"
}
if(grepl("mm9",getGenomeAnnotation(ArchRProj)$genome, ignore.case = TRUE)){
species <- "Mus musculus"
}
if(grepl("mm10",getGenomeAnnotation(ArchRProj)$genome, ignore.case = TRUE)){
species <- "Mus musculus"
}
}
#############################################################
# Get PWM List adapted from chromVAR!
#############################################################
.logDiffTime(paste0("Gettting Motif Set, Species : ", species), t1 = tstart, verbose = TRUE, logFile = logFile)
if(tolower(motifSet)=="jaspar2020"){
.requirePackage("JASPAR2020",installInfo='BiocManager::install("JASPAR2020")')
args <- list(species = species, collection = collection, ...)
motifs <- TFBSTools::getMatrixSet(JASPAR2020::JASPAR2020, args)
obj <- .summarizeJASPARMotifs(motifs)
motifs <- obj$motifs
motifSummary <- obj$motifSummary
}else if(tolower(motifSet)=="jaspar2018"){
.requirePackage("JASPAR2018",installInfo='BiocManager::install("JASPAR2018")')
args <- list(species = species, collection = collection, ...)
motifs <- TFBSTools::getMatrixSet(JASPAR2018::JASPAR2018, args)
obj <- .summarizeJASPARMotifs(motifs)
motifs <- obj$motifs
motifSummary <- obj$motifSummary
}else if(tolower(motifSet)=="jaspar2016"){
.requirePackage("JASPAR2016",installInfo='BiocManager::install("JASPAR2018")')
args <- list(species = species, collection = collection, ...)
motifs <- TFBSTools::getMatrixSet(JASPAR2016::JASPAR2016, args)
obj <- .summarizeJASPARMotifs(motifs)
motifs <- obj$motifs
motifSummary <- obj$motifSummary
}else if(tolower(motifSet)=="cisbp"){
.requirePackage("chromVARmotifs",installInfo='devtools::install_github("GreenleafLab/chromVARmotifs")')
if(tolower(species) == "mus musculus"){
if(version == 1){
message("Using version 1 motifs!")
data("mouse_pwms_v1")
motifs <- mouse_pwms_v1
}else if(version == 2){
message("Using version 2 motifs!")
data("mouse_pwms_v2")
motifs <- mouse_pwms_v2
}else{
stop("Only versions 1 and 2 exist!")
}
obj <- .summarizeChromVARMotifs(motifs)
motifs <- obj$motifs
motifSummary <- obj$motifSummary
}else if(tolower(species) == "homo sapiens"){
if(version == 1){
message("Using version 1 motifs!")
data("human_pwms_v1")
motifs <- human_pwms_v1
}else if(version == 2){
message("Using version 2 motifs!")
data("human_pwms_v2")
motifs <- human_pwms_v2
}else{
stop("Only versions 1 and 2 exist!")
}
obj <- .summarizeChromVARMotifs(motifs)
motifs <- obj$motifs
motifSummary <- obj$motifSummary
}else{
stop("Species not recognized homo sapiens, mus musculus supported by CisBP!")
}
}else if(tolower(motifSet)=="encode"){
.requirePackage("chromVARmotifs",installInfo='devtools::install_github("GreenleafLab/chromVARmotifs")')
data("encode_pwms")
motifs <- encode_pwms
obj <- .summarizeChromVARMotifs(motifs)
motifs <- obj$motifs
motifSummary <- obj$motifSummary
}else if(tolower(motifSet)=="homer"){
.requirePackage("chromVARmotifs",installInfo='devtools::install_github("GreenleafLab/chromVARmotifs")')
data("homer_pwms")
motifs <- homer_pwms
obj <- .summarizeChromVARMotifs(motifs)
motifs <- obj$motifs
motifSummary <- obj$motifSummary
}else if(tolower(motifSet)=="vierstra"){
if(tolower(collection)=="individual"){
url = "https://jeffgranja.s3.amazonaws.com/ArchR/Annotations/Vierstra_Individual_Motifs.rds"
message("Using Vierstra v1.0 motifs. See https://www.vierstra.org/resources/motif_clustering for more details.")
} else if(tolower(collection == "archetype")){
url = "https://jeffgranja.s3.amazonaws.com/ArchR/Annotations/Vierstra_Archetype_Motifs_v2.1.rds"
message("Using Vierstra v2.1beta motifs. See https://resources.altius.org/~jvierstra/projects/motif-clustering-v2.1beta/ for more details.")
} else {
stop(paste0("Error! collection ", collection, " not recognized for motifSet ",motifSet,
". Accepted values are 'individual' and 'archetype'"))
}
annoPath <- file.path(find.package("ArchR", NULL, quiet = TRUE), "data", "Annotations")
dir.create(annoPath, showWarnings = FALSE)
#Download
if(!file.exists(file.path(annoPath, basename(url)))){
message("Motif file ", basename(url)," does not exist! Downloading..")
download.file(
url = url,
destfile = file.path(annoPath, basename(url)),
quiet = FALSE
)
}
motifFile <- file.path(annoPath, basename(url))
motifs <- readRDS(motifFile)
obj <- NULL
motifSummary <- NULL
}else if(tolower(motifSet)=="custom"){
obj <- NULL
motifs <- motifPWMs
motifSummary <- NULL
}else{
stop("Error MotifSet Not Recognized!")
}
.logThis(motifs, "motifs", logFile = logFile)
.logThis(obj, "obj", logFile = logFile)
.logThis(motifSummary, "motifSummary", logFile = logFile)
#############################################################
# Get BSgenome Information!
#############################################################
genome <- ArchRProj@genomeAnnotation$genome
BSgenome <- eval(parse(text = genome))
BSgenome <- validBSgenome(BSgenome)
#############################################################
# Calculate Motif Positions
#############################################################
.logDiffTime("Finding Motif Positions with motifmatchr!", t1 = tstart, verbose = TRUE, logFile = logFile)
peakSet <- ArchRProj@peakSet
if(is.null(peakSet)){
.logStop("peakSet is NULL. You need a peakset to run addMotifAnnotations! See addReproduciblePeakSet!", logFile = logFile)
}
motifPositions <- motifmatchr::matchMotifs(
pwms = motifs,
subject = peakSet,
genome = BSgenome,
out = "positions",
p.cutoff = cutOff,
w = width
)
#############################################################
# Filter Motifs With No Matches
#############################################################
#Number of Overlaps
nO <- lapply(motifPositions, length) %>% unlist
mF <- names(which(nO == 0))
if(all(nO == 0)){
stop("No Overlaps Found! Please check your peakSet and genome!")
}
if(length(mF) > 0){
.logDiffTime(paste0("Filtering Motif Annotations with 0 overlaps :\n\n ", paste(mF, collapse=", "), "\n\n"), t1 = tstart, verbose = TRUE, logFile = logFile)
#Filter
motifPositions <- motifPositions[nO > 0]
motifSummary <- motifSummary[names(motifPositions),,drop=FALSE]
motifs <- motifs[names(motifPositions)]
}else{
.logDiffTime(paste0("All Motifs Overlap at least 1 peak!"), t1 = tstart, verbose = TRUE, logFile = logFile)
}
#############################################################
# Motif Overlap Matrix
#############################################################
.logDiffTime("Creating Motif Overlap Matrix", t1 = tstart, verbose = TRUE, logFile = logFile)
allPositions <- unlist(motifPositions)
overlapMotifs <- findOverlaps(peakSet, allPositions, ignore.strand=TRUE)
motifMat <- Matrix::sparseMatrix(
i = queryHits(overlapMotifs),
j = match(names(allPositions),names(motifPositions))[subjectHits(overlapMotifs)],
x = rep(TRUE, length(overlapMotifs)),
dims = c(length(peakSet), length(motifPositions))
)
colnames(motifMat) <- names(motifPositions)
motifMat <- SummarizedExperiment::SummarizedExperiment(assays=SimpleList(matches = motifMat), rowRanges = peakSet)
.logDiffTime("Finished Getting Motif Info!", t1 = tstart, verbose = TRUE, logFile = logFile)
out <- SimpleList(
motifSummary = motifSummary,
motifMatches = motifMat,
motifPositions = motifPositions,
motifList = motifs,
date = Sys.Date()
)
dir.create(file.path(getOutputDirectory(ArchRProj), "Annotations"), showWarnings=FALSE)
savePositions <- file.path(getOutputDirectory(ArchRProj), "Annotations", paste0(annoName,"-Positions-In-Peaks.rds"))
saveMatches <- file.path(getOutputDirectory(ArchRProj), "Annotations", paste0(annoName,"-Matches-In-Peaks.rds"))
ArchRProj@peakAnnotation[[annoName]]$Name <- annoName
ArchRProj@peakAnnotation[[annoName]]$motifs <- motifs
ArchRProj@peakAnnotation[[annoName]]$motifSummary <- motifSummary
ArchRProj@peakAnnotation[[annoName]]$Positions <- savePositions
ArchRProj@peakAnnotation[[annoName]]$Matches <- saveMatches
.safeSaveRDS(out, file.path(getOutputDirectory(ArchRProj), "Annotations", paste0(annoName,"-In-Peaks-Summary.rds")), compress = FALSE)
.safeSaveRDS(out$motifPositions, savePositions, compress = FALSE)
.safeSaveRDS(out$motifMatches, saveMatches, compress = FALSE)
.endLogging(logFile = logFile)
return(ArchRProj)
}
.summarizeJASPARMotifs <- function(motifs = NULL){
motifNames <- lapply(seq_along(motifs), function(x){
namex <- make.names(motifs[[x]]@name)
if(substr(namex,nchar(namex),nchar(namex))=="."){
namex <- substr(namex,1,nchar(namex)-1)
}
namex <- paste0(namex, "_", x)
namex
}) %>% unlist(.)
motifDF <- lapply(seq_along(motifs), function(x){
data.frame(
row.names = motifNames[x],
name = motifs[[x]]@name[[1]],
ID = motifs[[x]]@ID,
strand = motifs[[x]]@strand,
symbol = ifelse(!is.null(motifs[[x]]@tags$symbol[1]), motifs[[x]]@tags$symbol[1], NA) ,
family = ifelse(!is.null(motifs[[x]]@tags$family[1]), motifs[[x]]@tags$family[1], NA),
alias = ifelse(!is.null(motifs[[x]]@tags$alias[1]), motifs[[x]]@tags$alias[1], NA),
stringsAsFactors = FALSE
)
}) %>% Reduce("rbind", .) %>% DataFrame
names(motifs) <- motifNames
out <- list(motifs = motifs, motifSummary = motifDF)
return(out)
}
.summarizeChromVARMotifs <- function(motifs = NULL){
motifNames <- lapply(seq_along(motifs), function(x){
namex <- make.names(motifs[[x]]@name)
if(grepl("LINE", namex)){
splitNamex <- stringr::str_split(motifs[[x]]@ID, pattern="\\_", simplify = TRUE)
namex <- splitNamex[1, grep("LINE",splitNamex[1,]) + 1]
}
if(substr(namex,nchar(namex),nchar(namex))=="."){
namex <- substr(namex,1,nchar(namex)-1)
}
namex <- paste0(namex, "_", x)
namex
}) %>% unlist(.)
motifNames2 <- lapply(seq_along(motifs), function(x){
namex <- make.names(motifs[[x]]@name)
if(grepl("LINE", namex)){
splitNamex <- stringr::str_split(motifs[[x]]@ID, pattern="\\_", simplify = TRUE)
namex <- splitNamex[1, grep("LINE",splitNamex[1,]) + 1]
}
if(substr(namex,nchar(namex),nchar(namex))=="."){
namex <- substr(namex,1,nchar(namex)-1)
}
namex
}) %>% unlist(.)
motifDF <- lapply(seq_along(motifs), function(x){
df <- data.frame(
row.names = motifNames[x],
name = motifNames2[[x]],
ID = motifs[[x]]@ID,
strand = motifs[[x]]@strand,
stringsAsFactors = FALSE
)
}) %>% Reduce("rbind", .) %>% DataFrame
names(motifs) <- motifNames
out <- list(motifs = motifs, motifSummary = motifDF)
return(out)
}
#' Add ArchR annotations to an ArchRProject
#'
#' This function adds information about which peaks in the ArchR database contain input regions to a given ArchRProject.
#' For each peak, a binary value is stored indicating whether each region is observed within the peak region.
#'
#' @param ArchRProj An `ArchRProject` object.
#' @param db A string indicating the database or a path to a database to use for peak annotation. Options include ArchR,
#' LOLA, and a valid path to a file of class `ArchRAnno`.
#' @param collection A string indicating which collection within the database to collect for annotation.
#' For ArchR, options are "ATAC", "EncodeTFBS", "CistromeTFBS", or "Codex".
#' For LOLA, options include "EncodeTFBS" "CistromeTFBS", "CistromeEpigenome", "Codex", or "SheffieldDnase".
#' If supplying a custom `ArchRAnno` file please select a valid collection from within that database.
#' @param name The name of the `peakAnnotation` object to be stored in the `ArchRProject`.
#' @param force A boolean value indicating whether to force the `peakAnnotation` object indicated by `name` 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.
#' @export
addArchRAnnotations <- function(
ArchRProj = NULL,
db = "ArchR",
collection = "EncodeTFBS",
name = collection,
force = FALSE,
logFile = createLogFile("addArchRAnnotations")
){
.validInput(input = ArchRProj, name = "ArchRProj", valid = c("ArchRProj"))
.validInput(input = db, name = "db", valid = c("character"))
.validInput(input = collection, name = "collection", valid = c("character"))
.validInput(input = name, name = "name", valid = c("character"))
.validInput(input = force, name = "force", valid = c("boolean"))
.validInput(input = logFile, name = "logFile", valid = c("character"))
tstart <- Sys.time()
.startLogging(logFile = logFile)
.logThis(mget(names(formals()),sys.frame(sys.nframe())), "addArchRAnnotations Input-Parameters", logFile = logFile)
if(name %in% names(ArchRProj@peakAnnotation)){
if(force){
message("peakAnnotation name already exists! Overriding.")
}else{
stop("peakAnnotation name already exists! set force = TRUE to override!")
}
}
genome <- tolower(tryCatch({
validBSgenome(getGenome(ArchRProj))$provider_version
}, error = function(e){
strsplit(validBSgenome(getGenome(ArchRProj))@pkgname,"\\.")[[1]][4]
}))
annoPath <- file.path(find.package("ArchR", NULL, quiet = TRUE), "data", "Annotations")
dir.create(annoPath, showWarnings = FALSE)
if(tolower(db) == "lola"){
if(genome == "hg19"){
url <- "https://jeffgranja.s3.amazonaws.com/ArchR/Annotations/LOLA-Hg19-v1.Anno"
}else if(genome == "hg38"){
url <- "https://jeffgranja.s3.amazonaws.com/ArchR/Annotations/LOLA-Hg38-v1.Anno"
}else if(genome == "mm9"){
url <- "https://jeffgranja.s3.amazonaws.com/ArchR/Annotations/LOLA-Mm9-v1.Anno"
}else if(genome == "mm10"){
url <- "https://jeffgranja.s3.amazonaws.com/ArchR/Annotations/LOLA-Mm10-v1.Anno"
}
#Download
if(!file.exists(file.path(annoPath, basename(url)))){
message("Annotation ", basename(url)," does not exist! Downloading..")
download.file(
url = url,
destfile = file.path(annoPath, basename(url)),
quiet = FALSE
)
}
AnnoFile <- file.path(annoPath, basename(url))
}else if(tolower(db) == "archr"){
if(genome == "hg19"){
url <- "https://jeffgranja.s3.amazonaws.com/ArchR/Annotations/ArchR-Hg19-v1.Anno"
}else if(genome == "hg38"){
url <- "https://jeffgranja.s3.amazonaws.com/ArchR/Annotations/ArchR-Hg38-v1.Anno"
}else if(genome == "mm9"){
stop("ArchR mm9 annotations not yet supported! Try LOLA for now!")
url <- "https://jeffgranja.s3.amazonaws.com/ArchR/Annotations/ArchR-Mm9-v1.Anno"
}else if(genome == "mm10"){
stop("ArchR mm10 annotations not yet supported! Try LOLA for now!")
url <- "https://jeffgranja.s3.amazonaws.com/ArchR/Annotations/ArchR-Mm10-v1.Anno"
}
#Download
if(!file.exists(file.path(annoPath, basename(url)))){
oldTimeout <- getOption('timeout')
options(timeout=10000)
message("Annotation ", basename(url)," does not exist! Downloading..")
download.file(
url = url,
destfile = file.path(annoPath, basename(url)),
quiet = FALSE
)
options(timeout=oldTimeout)
}
AnnoFile <- file.path(annoPath, basename(url))
}else if(tolower(db) %ni% c("archr", "lola")){
if(!file.exists(db)){
stop("Database path does not exist! Please supply valid database for Annotations!")
}
AnnoFile <- db
}else{
stop("Please supply valid database for Annotations!")
}
#Check AnnoFile is ArchRAnno
if (h5read(AnnoFile, "Class") != "ArchRAnno") {
stop("Not Valid ArchRAnno!")
}
#Check if Collection is Valid
h5d <- h5ls(AnnoFile)
collections <- h5d[h5d$group == "/" & h5d$otype == "H5I_GROUP",]$name
if(any(tolower(collections) == tolower(collection))){
collection <- collections[tolower(collections) %in% tolower(collection)]
}else{
stop("Not Valid Collection in ArchRAnno Database!")
}
#############################################################
# Peak Overlap Matrix
#############################################################
peakSet <- getPeakSet(ArchRProj)
if(is.null(peakSet)){
.logStop("peakSet is NULL. You need a peakset to run addMotifAnnotations! See addReproduciblePeakSet!", logFile = logFile)
}
chr <- paste0(unique(seqnames(peakSet)))
.logMessage("Annotating Chromosomes", verbose = TRUE, logFile = logFile)
regionMat <- lapply(seq_along(chr), function(i){
.logMessage(paste0("\tAnnotating Chr: ", chr[i]), verbose = TRUE, logFile = logFile)
regions <- .getRegionsFromAnno(AnnoFile = AnnoFile, Group = collection, chr = chr[i])
o <- DataFrame(findOverlaps(query = peakSet, subject = regions, ignore.strand = TRUE))
o$ID <- as.integer(mcols(regions)[o$subjectHits, "ID"])
o$subjectHits <- NULL
o
}) %>% Reduce("rbind", .)
.logThis(regionMat, "regionMat-Overlaps", logFile=logFile)
.logThis(range(regionMat[, 1]), "regionMat-Overlaps-1", logFile=logFile)
.logThis(range(regionMat[, 2]), "regionMat-Overlaps-2", logFile=logFile)
.logThis(peakSet, "regionMat-Overlaps-1-Peaks", logFile=logFile)
.logThis(unique(regionMat$ID), "regionMat-Overlaps-2-IDs", logFile=logFile)
regionMat <- Matrix::sparseMatrix(
i = regionMat[, 1],
j = regionMat[, 2],
x = rep(TRUE, nrow(regionMat)),
dims = c(length(peakSet), max(regionMat$ID))
)
.logThis(regionMat, "regionMat", logFile=logFile)
#Get Region Metadata
regionMetadata <- DataFrame(h5read(AnnoFile, paste0(collection,"/Info")))
rownames(regionMetadata) <- regionMetadata$name
colnames(regionMat) <- rownames(regionMetadata)
regionMetadata$name <- NULL
#Matches Summarized Experiment
regionMat <- SummarizedExperiment::SummarizedExperiment(
assays=SimpleList(matches = regionMat),
rowRanges = peakSet,
colData = regionMetadata
)
.logThis(regionMat, "regionSE", logFile=logFile)
#############################################################
# Filter Regions With No Matches
#############################################################
#Number of Overlaps
nO <- Matrix::colSums(assay(regionMat))
rF <- names(which(nO == 0))
if(all(nO == 0)){
stop("No Overlaps Found! Please check your peakSet and genome!")
}
if(length(rF) > 0){
.logDiffTime(paste0("Filtering Region Annotations with 0 overlaps :\n\n ", paste(rF, collapse=", "), "\n\n"), t1 = tstart, verbose = TRUE, logFile = logFile)
#Filter
regionMat <- regionMat[,nO > 0,drop=FALSE]
}else{
.logDiffTime(paste0("All Regions Overlap at least 1 peak!"), t1 = tstart, verbose = TRUE, logFile = logFile)
}
#############################################################
# Save
#############################################################
dir.create(file.path(getOutputDirectory(ArchRProj), "Annotations"), showWarnings=FALSE)
saveMatches <- file.path(getOutputDirectory(ArchRProj), "Annotations", paste0(name,"-Matches-In-Peaks.rds"))
out <- SimpleList(
regionMatches = regionMat,
regionPositions = "None",
date = Sys.Date()
)
ArchRProj@peakAnnotation[[name]]$Name <- name
ArchRProj@peakAnnotation[[name]]$Positions <- "None"
ArchRProj@peakAnnotation[[name]]$Matches <- saveMatches
.safeSaveRDS(out, file.path(getOutputDirectory(ArchRProj), "Annotations", paste0(name,"-In-Peaks-Summary.rds")), compress = FALSE)
.safeSaveRDS(out$regionMatches, saveMatches, compress = FALSE)
.endLogging(logFile = logFile)
return(ArchRProj)
}
.getRegionsFromAnno <- function(
AnnoFile = NULL,
Group = NULL,
chr = NULL,
out = "GRanges",
method = "fast"
){
if(is.null(chr)){
stop("Need to provide chromosome to read!")
}
o <- h5closeAll()
if (h5read(AnnoFile, "Class") != "ArchRAnno") {
stop("Not Valid ArchRAnno!")
}
if(chr %ni% .availableSeqnames(AnnoFile, Group)){
stop(paste("Error! Chromosome ",chr," not in AnnoFile!"))
}
o <- h5closeAll()
nRegions <- sum(.h5read(AnnoFile, paste0(Group,"/",chr,"/IDLengths"), method = method))
if(nRegions==0){
if(tolower(out)=="granges"){
output <- GRanges(seqnames = chr, IRanges(start = 1, end = 1), ID = "tmp")
output <- output[-1,]
}else{
output <- IRanges(start = 1, end = 1)
mcols(output)$ID <- c("tmp")
output <- output[-1,]
}
return(output)
}
if(tolower(method) == "fast"){
output <- .h5read(AnnoFile, paste0(Group,"/",chr,"/Ranges"), method = method) %>%
{IRanges(start = .[,1], width = .[,2])}
mcols(output)$ID <- Rle(
values = .h5read(AnnoFile, paste0(Group,"/",chr,"/IDValues"), method = method),
lengths = .h5read(AnnoFile, paste0(Group,"/",chr,"/IDLengths"), method = method)
)
}else{
o <- h5closeAll()
idRle <- Rle(h5read(AnnoFile, paste0(Group,"/",chr,"/IDValues")), h5read(AnnoFile, paste0(Group,"/",chr,"/IDLengths")))
idx <- seq_along(idRle)
if(length(idx) > 0){
output <- h5read(AnnoFile, paste0(Group,"/",chr,"/Ranges"), index = list(idx, 1:2)) %>%
{IRanges(start = .[,1], width = .[,2])}
mcols(output)$ID <- idRle[idx]
}else{
output <- IRanges(start = 1, end = 1)
mcols(output)$ID <- c("tmp")
output <- output[-1,]
}
}
o <- h5closeAll()
if(tolower(out)=="granges"){
if(length(output) > 0){
output <- GRanges(seqnames = chr, ranges(output), ID = mcols(output)$ID)
}else{
output <- IRanges(start = 1, end = 1)
mcols(output)$ID <- c("tmp")
output <- GRanges(seqnames = chr, ranges(output), ID = mcols(output)$ID)
output <- output[-1,]
}
}
return(output)
}
#' Peak Annotation Hypergeometric Enrichment in Marker Peaks.
#'
#' This function will perform hypergeometric enrichment of a given peak annotation within the defined marker peaks.
#'
#' @param seMarker A `SummarizedExperiment` object returned by `markerFeatures()`.
#' @param ArchRProj An `ArchRProject` object.
#' @param peakAnnotation A `peakAnnotation` object in the provided `ArchRProject` to be used for hypergeometric testing.
#' @param matches A custom `peakAnnotation` matches object used as input for the hypergeometric test. See
#' `motifmatchr::matchmotifs()` for additional information.
#' @param cutOff A valid-syntax logical statement that defines which marker features from `seMarker` to use.
#' `cutoff` can contain any of the `assayNames` from `seMarker`.
#' @param background A string that indicates whether to use a background set of matched peaks to compare against ("bgdPeaks") or all peaks ("all").
#' @param logFile The path to a file to be used for logging ArchR output.
#' @export
peakAnnoEnrichment <- function(
seMarker = NULL,
ArchRProj = NULL,
peakAnnotation = NULL,
matches = NULL,
cutOff = "FDR <= 0.1 & Log2FC >= 0.5",
background = "all",
logFile = createLogFile("peakAnnoEnrichment")
){
.validInput(input = seMarker, name = "seMarker", valid = c("SummarizedExperiment"))
.validInput(input = ArchRProj, name = "ArchRProj", valid = c("ArchRProj"))
.validInput(input = peakAnnotation, name = "peakAnnotation", valid = c("character", "null"))
.validInput(input = matches, name = "matches", valid = c("SummarizedExperiment", "null"))
.validInput(input = cutOff, name = "cutOff", valid = c("character"))
.validInput(input = background, name = "background", valid = c("character"))
.validInput(input = logFile, name = "logFile", valid = c("character"))
tstart <- Sys.time()
.startLogging(logFile = logFile)
.logThis(mget(names(formals()),sys.frame(sys.nframe())), "peakAnnoEnrichment Input-Parameters", logFile = logFile)
if(metadata(seMarker)$Params$useMatrix != "PeakMatrix"){