Sample specific enhancer identificiation

[ferenckata]

Hei,

As far as I can see, the enhancer calling does not provide sample-specific enhancers, so I used a function from CAGEfightR to extract sample-specific enhancer bed files. See below. Let me know if there is a shorter way, or one that provides also the tpms per enhancer per sample.

brcage <- CAGEr::quickEnhancers(brcage)
supported_enhancers <- CAGEfightR::subsetBySupport(
        brcage[["enhancers"]],
        inputAssay="counts",
        unexpressed=0,
        minSamples=1)
sample_per_enhancer <- supported_enhancers@assays@data$counts
for (sample_name in colnames(sample_per_enhancer)){
        sample_bed <- lapply(
            names(
                sample_per_enhancer[
                    # filter for enhancers with non-zero tags per sample
                    sample_per_enhancer[,sample_name]>0,][,sample_name]
                ),
            # extract chr and coordinates into separate entities
            function(x){
                unlist(strsplit(x, ":|-"))
                }
        )
        # save list of coordinates to bedfile
        sink(file.path(
            cagerFolder,
            "enhancers",
            paste0(sample_name, "_enhancers.bed")))
        for (line in sample_bed){
            cat(paste0(line[1], "\t", line[2], "\t", line[3], "\n"))
            }
        sink()
}