ConfigFeatures.GRanges: QcConfigFeatures.GRanges

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

QcConfigFeatures.GRanges

Description

QcConfigFeatures.GRanges

Usage

ConfigFeatures.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

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