ClusteredSignal_TSNE.fromConfig: ClusteredSignal_TSNE.fromConfig

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

ClusteredSignal_TSNE.fromConfig

Description

ClusteredSignal_TSNE.fromConfig

Usage

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

Value

A ClusteredSignal_TSNE object containing clustering and TSNE information.

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)

query_gr = feature_config$assessment_features$CTCF_features
sclust = ClusteredSignal_TSNE.fromConfig(sqc$signal_config, sqc$features_config$assessment_features)
sclust$

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