ConfigFeatures.files: QcConfigFeatures
In jrboyd/seqtsne: Application of t-sne to NGS Genomic Signal Profiles

ConfigFeatures.files

R Documentation

QcConfigFeatures

Description

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

Usage

ConfigFeatures.files(
  file_paths,
  file_paths.input = character(),
  run_separately = TRUE,
  sample_names = NULL,
  sample_names.split = NULL,
  group_names = NULL,
  group_name.input = "input",
  group_colors = NULL,
  feature_load_FUN = NULL,
  n_peaks = 1000,
  balance_groups = FALSE,
  overlap_extension = 0,
  consensus_fraction = getOption("SQC_CONSENSUS_FRACTION", 0),
  consensus_n = getOption("SQC_CONSENSUS_N", 1),
  process_features = getOption("SQC_PROCESS_FEATURES", TRUE)
)

Arguments

`file_paths`	character paths to files
`run_separately`	If TRUE, each item is considered a separate group. Default is TRUE.
`group_names`	vector of group names to assign from according to groups
`group_colors`	vector of colors to use per group
`feature_load_FUN`	function that takes a vector of file paths and returns list of GRanges.
`n_peaks`	number of peaks to subset for
`balance_groups`	If TRUE, will attempt to represent imbalanced groups more equally
`overlap_extension`	bp to extends regions by before calculating overlaps
`consensus_fraction`	A numeric between 0 and 1 specifying the fraction of grs that must overlap to be considered consensus.
`consensus_n`	An integer number specifying the absloute minimum of input grs that must overlap for a site to be considered consensus.
`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

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.