ConfigFeatures.parse: QcConfigFeatures

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

QcConfigFeatures

Description

See the example feature config file system.file(package = "ssvQC", "extdata/ssvQC_peak_config.csv").

Usage

ConfigFeatures.parse(
  feature_config_file,
  process_features = getOption("SQC_PROCESS_FEATURES", TRUE)
)

Arguments

feature_config_file	A valid feature config file.
process_features	if TRUE, features are loaded and overlapped to generate assement regions as part of creating QcConfigFeatures object

Details

Or create a config file using QcConfigFeatures.save_config after making one using a different method.

Value

QcConfigFeatures object

QcConfigFeatures object

a QcConfigFeatures object

A QcConfigFeatures object

Invisibly returns path to written config file.

Slots

feature_load_FUN

function.

n_peaks

numeric.

consensus_fraction

numeric.

consensus_n

numeric.

Examples

feature_config_file = system.file(package = "ssvQC", "extdata/ssvQC_peak_config.csv")
config_df = .parse_config_body(feature_config_file)
config_df$file = file.path(system.file(package = "ssvQC", "extdata"), config_df$file)
feature_conf = QcConfigFeatures(config_df, process_features = TRUE)
QcConfigFeatures.null()
np_files = dir(system.file(package = "ssvQC", "extdata"), pattern = "Peak$", full.names = TRUE)
object = QcConfigFeatures.files(np_files, balance_groups = TRUE)
object = ssvQC.prepFeatures(object)
plot(object)

object = QcConfigFeatures.files(np_files, 
  group_names = c("10A", "AT1", "CA1"), 
  sample_names = c("MCF10A_CTCF", "MCF10AT1_CTCF", "MCF10CA1a_CTCF"))
object = ssvQC.prepFeatures(object)
plot(object)
feature_config_file = system.file(package = "ssvQC", "extdata/ssvQC_peak_config.csv")
object = QcConfigFeatures.parse(feature_config_file)
plot(object)
feature_config_file = system.file(package = "ssvQC", "extdata/ssvQC_peak_config.csv")
feature_config = QcConfigFeatures.parse(feature_config_file)

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