QcConfigFeatures.GRanges: QcConfigFeatures.GRanges

View source: R/QcConfigFeatures.R

QcConfigFeatures.GRangesR Documentation

QcConfigFeatures.GRanges

Description

QcConfigFeatures.GRanges

Usage

QcConfigFeatures.GRanges(
  query_gr,
  n_peaks = 2000,
  run_separately = TRUE,
  sample_names = NULL,
  sample_names.split = NULL,
  group_names = NULL,
  group_colors = NULL,
  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

query_gr

either a list of GRanges of a GRanges object. GRanges object will be handled differently if its mcols are a membership table as generated by seqsetvis::sssvOverlapIntervalSets or seqsetvis::ssvConsensusIntervalSets.

n_peaks

number of peaks to subset for

run_separately

If TRUE, each item is considered a separate group. Default is TRUE.

sample_names

Unique names to use per GRanges in list or columns in membership table. Do not set if single GRanges does not have memb table.

sample_names.split

Unique names to use per GRanges in list or columns in membership table. Do not set if single GRanges does not have memb table.

group_names

vector of group names to assign from according to groups

group_colors

vector of colors to use per group

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

Value

A QcConfigFeatures object based only on input query_gr.

Examples

np_file = system.file("extdata/MCF10A_CTCF_random100.narrowPeak", package = "ssvQC")
query_gr = seqsetvis::easyLoad_narrowPeak(np_file)[[1]]
qc_feature.gr = QcConfigFeatures.GRanges(query_gr)
qc_feature.gr

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