getRegions {dStruct}R Documentation

Constructs potential differentially reactive regions.

Description

This function takes between- and within-group d scores for a transcript as input and identifies regions where the former is generally larger. Regions that pass minimum quality and minimum signal criteria are returned.

Usage

getRegions(
  d_within,
  d_spec,
  rdf,
  min_length = 11,
  check_signal_strength = TRUE,
  check_nucs = TRUE,
  check_quality = TRUE,
  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.

Value

Integer vector of nucleotides that constitute potential differentially reactive regions.

Author(s)

Krishna Choudhary

References

Choudhary, K., Lai, Y. H., Tran, E. J., & Aviran, S. (2019). dStruct: identifying differentially reactive regions from RNA structurome profiling data. Genome biology, 20(1), 1-26.


[Package dStruct version 1.0.0 Index]