ssvQC.selectClusters: ssvQC.removeClusters

In FrietzeLabUVM/ssvQC: QC for enrichment based NGS

ssvQC.removeClusters

Description

ssvQC.removeClusters

ssvQC.selectClusters

Usage

ssvQC.removeClusters(
  sqc,
  cluster_numbers,
  features_name = NULL,
  signals_name = NULL,
  invert = FALSE
)

ssvQC.selectClusters(
  sqc,
  cluster_numbers,
  features_name = NULL,
  signals_name = NULL,
  invert = FALSE
)

Arguments

sqc	A valid ssvQC object after clustering by ssvQC.prepSignal
cluster_numbers	Number for clusters.
features_name	feature_name to perform selection on. Required if multiple feature sets present.
signals_name	signal_name to perform selection on. Required if multiple signal sets present.
invert	If true, flip removal to selection and vice versa.

Value

ssvQC object with selected clusters removed.

Examples

library(ssvQC)
options(mc.cores = 1)
set.seed(0)
features_config_file = system.file(package = "ssvQC", "extdata/ssvQC_peak_config.csv")
features_config = QcConfigFeatures.parse(features_config_file)

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

sqc.complete.file = ssvQC(features_config_file, bam_config_file)

sqc.complete = ssvQC(features_config, bam_config)
sqc = ssvQC.runAll(sqc.complete)
sqc$plots$signal$heatmaps$CTCF_features$CTCF_signal

sqc.rmclust = ssvQC.removeClusters(sqc, cluster_numbers = 1:4)
sqc.rmclust$plots$signal$heatmaps$CTCF_features$CTCF_signal

sqc.rmclust_inv = ssvQC.removeClusters(sqc, cluster_numbers = 1:4, invert = TRUE)
sqc.rmclust_inv$plots$signal$heatmaps$CTCF_features$CTCF_signal

sqc.selclust = ssvQC.selectClusters(sqc, cluster_numbers = 1:4)
sqc.selclust$plots$signal$heatmaps$CTCF_features$CTCF_signal

sqc.selclust_inv = ssvQC.selectClusters(sqc, cluster_numbers = 1:4, invert = TRUE)
sqc.selclust_inv$plots$signal$heatmaps$CTCF_features$CTCF_signal

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