ClusteredSignal_TSNE: ClusteredSignal_TSNE

In jrboyd/seqtsne: Application of t-sne to NGS Genomic Signal Profiles

ClusteredSignal_TSNE

Description

ClusteredSignal_TSNE

Usage

ClusteredSignal_TSNE(
  signal_profile_dt,
  query_gr,
  manual_assigned = list(),
  nclust = 6,
  signal_var = "y",
  signal_var.within = "y",
  facet_var = "name_split",
  extra_var = character()
)

Arguments

signal_profile_dt	Tidy data.table containing profile information. See output of seqsetvis::ssvFetchBam.
query_gr	A GRanges containing regions to retrieve signal data at.
manual_assigned	NYI but should allow manual cluster assignment.
nclust	Number of k-means clusters to calculate. Default is 6.
signal_var	Variable name for signal information to cluster upon in signal_profile_dt. Default is "y".
signal_var.within	Variable name for ranking items within clusters. The Default is the same as signal_var.
facet_var	Variable that will eventually be used in heatmap facets. Ensures it is preserved and not aggregated away. Default is "name_split".
extra_var	Any extra variables to preserve and avaoid aggregating away.
bfc	BiocFileCache to use, uses default location otherwise.

Value

A ClusteredSignal_TSNE object containing clustering and TSNE information.

Examples

signal_profile_dt = seqsetvis::CTCF_in_10a_profiles_dt
setnames(signal_profile_dt, "sample", "name_split")
query_gr = seqsetvis::CTCF_in_10a_overlaps_gr
clust_sig = ClusteredSignal_TSNE(signal_profile_dt, query_gr)

jrboyd/seqtsne documentation built on Nov. 5, 2022, 6:37 a.m.