ssvQC.removeFeatures: ssvQC.selectFeatures

In FrietzeLabUVM/ssvQC: QC for enrichment based NGS

ssvQC.selectFeatures

Description

ssvQC.selectFeatures

ssvQC.removeFeatures

Usage

ssvQC.selectFeatures(
  sqc,
  ids = NULL,
  grs = NULL,
  features_name = NULL,
  invert = FALSE
)

ssvQC.removeFeatures(
  sqc,
  ids = NULL,
  grs = NULL,
  features_name = NULL,
  invert = FALSE
)

Arguments

sqc	A valid ssvQC object after clustering by ssvQC.prepSignal
ids	region ids.
grs	GRanges to use to fine region ids.
invert	If true, flip removal to selection and vice versa.

Value

ssvQC object with selected regions 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)
ids = c("region_1", "region_2")
grs = NULL
invert = FALSE
features_name = NULL

sqc$plots$SCC$dots

#removal
sqc.filtered = ssvQC.removeFeatures(sqc, ids = c("region_1", "region_2"))

sqc.filtered2 = ssvQC.removeFeatures(sqc.filtered, ids = c("region_1", "region_2"))

sqc.filtered.inv = ssvQC.removeFeatures(sqc, ids = c("region_1", "region_2", "region_3", "region_4", "region_5"), invert = TRUE)

sqc.filtered.gr = ssvQC.removeFeatures(sqc, grs = GRanges(paste0("chr", 1:16), IRanges(1, 1e9)))
sqc.filtered.gr$features_config$assessment_features
sqc.filtered.gr$plots$signal$heatmaps
sqc.filtered.gr$plots$SCC$dots

sqc.filtered.gr_inv = ssvQC.removeFeatures(sqc, grs = GRanges(paste0("chr", 1:16), IRanges(1, 1e9)), invert = TRUE)
sqc.filtered.gr_inv$features_config$assessment_features
sqc.filtered.gr_inv$plots$signal$heatmaps
sqc.filtered.gr_inv$plots$SCC$dots

# selection
sqc.selected = ssvQC.selectFeatures(sqc, ids = c("region_1", "region_2", "region_3", "region_4", "region_5"))

sqc.selected2 = ssvQC.selectFeatures(sqc.selected, ids = c("region_1", "region_2", "region_3", "region_4", "region_5"))

sqc.selected.inv = ssvQC.selectFeatures(sqc, ids = c("region_1", "region_2", "region_3", "region_4", "region_5"), invert = TRUE)

sqc.selected.gr = ssvQC.selectFeatures(sqc, grs = GRanges(paste0("chr", 1:16), IRanges(1, 1e9)))
sqc.selected.gr$features_config$assessment_features
sqc.selected.gr$plots$signal$heatmaps
sqc.selected.gr$plots$SCC$dots

sqc.selected.gr_inv = ssvQC.selectFeatures(sqc, grs = GRanges(paste0("chr", 1:16), IRanges(1, 1e9)), invert = TRUE)
sqc.selected.gr_inv$features_config$assessment_features
sqc.selected.gr_inv$plots$signal$heatmaps
sqc.selected.gr_inv$plots$SCC$dots

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