annotate_gr_clusters: annotate_gr_clusters

In jrboyd/ssvRecipes: Recipes using seqsetvis

annotate_gr_clusters

Description

annotate_gr_clusters

Usage

annotate_gr_clusters(qgr, clust_assign, tss_gr, max_dist = 5000)

Arguments

qgr
clust_assign	A data.frame derived from ssvSignalClustering output (clust_assign = unique(clust_dt[, .(id, cluster_id)]))

Examples

clust_dt = ssvSignalClustering(CTCF_in_10a_profiles_dt)
clust_dt.assign = unique(clust_dt[, .(id, cluster_id)])
qgr = CTCF_in_10a_overlaps_gr

tx_gr = rtracklayer::import.gff("~/gencode.v36.annotation.gtf",
                                feature.type = "transcript", format = "gtf")
tss_gr = GenomicRanges::promoters(tx_gr, 1, 0)

annotate_gr(qgr, tss_gr, max_dist = 1e4)
gls = annotate_gr_clusters(qgr, clust_dt.assign, tss_gr, max_dist = 1e4)

jrboyd/ssvRecipes documentation built on May 22, 2022, 7:07 a.m.