getRegions: Constructs potential differentially reactive regions.

In AviranLab/dStruct: Identifying differentially reactive regions from RNA structurome profiling data

Description

Constructs potential differentially reactive regions.

Usage

getRegions(d_within, d_spec, rdf, min_length = 11,
  check_signal_strength = T, check_nucs = T, check_quality = T,
  quality = 0.5, evidence = 0, signal_strength = 0.1)

Arguments

d_within	Nucleotide-wise d score for within-group variation.
d_spec	Nucleotide-wise d score for between-group variation.
rdf	Dataframe of reactivities for each sample.
min_length	Minimum length of constructed regions.
check_signal_strength	Logical, if TRUE, construction of regions must be based on nucleotides that have a minimum absolute value of reactivity.
check_nucs	Logical, if TRUE, constructed regions must have a minimum number of nucleotides participating in Wilcoxon signed rank test.
check_quality	Logical, if TRUE, check constructed regions for quality.
quality	Worst allowed quality for a region to be tested.
evidence	Minimum evidence of increase in variation from within-group comparisons to between-group comparisons for a region to be tested.
signal_strength	Threshold for minimum signal strength.

AviranLab/dStruct documentation built on Jan. 27, 2021, 2:28 a.m.