write_ssvQC: write_ssvQC.per_peak

In FrietzeLabUVM/ssvQC: QC for enrichment based NGS

write_ssvQC.per_peak

Description

write_ssvQC.per_peak

write_ssvQC.summary

Usage

write_ssvQC.per_peak(sqc, out_dir = getwd())

write_ssvQC.summary(sqc, out_dir = getwd())

write_ssvQC.correlation(sqc, out_dir = getwd())

Arguments

sqc	A valid ssvQC object, FRIP and SCC must be present.
out_dir	Output directory path. Defaults to current directory.

Value

invisibly returns paths to per peak QC files.

Examples

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 = ssvQC(features_config, bam_config)
sqc = ssvQC.runAll(sqc)
out = tempdir()
qc_files.per_peak = write_ssvQC.per_peak(sqc, out)
qc_files.summary = write_ssvQC.summary(sqc, out)
qc_files.correlation = write_ssvQC.correlation(sqc, out)
dir(out)

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