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add ability to get negative correlations #1688

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Merged
rcorces merged 1 commit into from
Oct 19, 2022
Merged

add ability to get negative correlations #1688

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12 changes: 10 additions & 2 deletions R/IntegrativeAnalysis.R
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Original file line number Diff line number Diff line change
Expand Up @@ -1380,7 +1380,10 @@ addPeak2GeneLinks <- function(
#' This function obtains peak-to-gene links from an ArchRProject.
#'
#' @param ArchRProj An `ArchRProject` object.
#' @param corCutOff A numeric describing the minimum numeric peak-to-gene correlation to return.
#' @param corCutOff A numeric describing the minimum numeric peak-to-gene correlation to return. If this value
#' is positive, then only positive correlations greater than or equal to `corCutOff` will be returned. If this value is
#' negative, then only negative correlations less than or equal to `corCutOff` will be returned. If `corCutOff = 0`, only
#' positive correlations will be returned.
#' @param FDRCutOff A numeric describing the maximum numeric peak-to-gene false discovery rate to return.
#' @param varCutOffATAC A numeric describing the minimum variance quantile of the ATAC peak accessibility when selecting links.
#' @param varCutOffRNA A numeric describing the minimum variance quantile of the RNA gene expression when selecting links.
Expand Down Expand Up @@ -1429,7 +1432,12 @@ getPeak2GeneLinks <- function(
}else{

p2g <- S4Vectors::metadata(ArchRProj@peakSet)$Peak2GeneLinks
p2g <- p2g[which(p2g$Correlation >= corCutOff & p2g$FDR <= FDRCutOff), ,drop=FALSE]
if(corCutOff >= 0) {
p2g <- p2g[which(p2g$Correlation >= corCutOff & p2g$FDR <= FDRCutOff), ,drop=FALSE]
} else {
p2g <- p2g[which(p2g$Correlation <= corCutOff & p2g$FDR <= FDRCutOff), ,drop=FALSE]
}


if(!is.null(varCutOffATAC)){
p2g <- p2g[which(p2g$VarQATAC > varCutOffATAC),]
Expand Down