ClusteredSignal.fromConfig: ClusteredSignal.fromConfig

In FrietzeLabUVM/ssvQC: QC for enrichment based NGS

ClusteredSignal.fromConfig

Description

ClusteredSignal.fromConfig

Usage

ClusteredSignal.fromConfig(
  signal_config,
  query_gr,
  manual_assigned = list(),
  nclust = 6,
  facet_var = "name_split",
  extra_var = character(),
  bfc = new_cache()
)

Arguments

signal_config	A valid QcConfigSignal
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.
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 object containing clustered signal profiles.

Examples

options(mc.cores = 10)
set.seed(0)
feature_config_file = system.file(package = "ssvQC", "extdata/ssvQC_peak_config.csv")
feature_config = QcConfigFeatures.parse(feature_config_file, process_features= TRUE)

bam_config_file = system.file(package = "ssvQC", "extdata/ssvQC_bam_config.csv")
bam_config = QcConfigSignal.parse(bam_config_file)

sqc = ssvQC(feature_config, bam_config)

prepS
query_gr = feature_config$assessment_features$CTCF_features
sclust = ClusteredSignal(sqc@signal_profile, sqc@feature_config$assessment_features)
sclust$

FrietzeLabUVM/ssvQC documentation built on March 25, 2024, 12:24 a.m.