dStruct: Performs de novo discovery of differentially reactive...

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

Description

Performs de novo discovery of differentially reactive regions.

Usage

dStruct(rdf, reps_A, reps_B, batches = F, min_length = 11,
  check_signal_strength = T, check_nucs = T, check_quality = T,
  quality = "auto", evidence = 0, signal_strength = 0.1,
  within_combs = NULL, between_combs = NULL, ind_regions = T, gap = 1,
  get_FDR = T, proximity_assisted = F, proximity = 10,
  proximity_defined_length = 30)

Arguments

rdf	Dataframe of reactivities for each sample.
reps_A	Number of replicates of group A.
reps_B	Number of replicates of group B.
batches	Logical suggesting if replicates of group A and B were performed in batches and are labelled accordingly. If TRUE, a heterogeneous/homogeneous subset may not have multiple samples from the same batch.
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.
within_combs	Data.frame with each column containing groupings of replicates of groups A or B, which will be used to assess within-group variation.
between_combs	Dataframe with each column containing groupings of replicates of groups A and B, which will be used to assess between-group variation.
ind_regions	Logical, if TRUE, test each region found in the transcript separately.
gap	Integer. Join regions if they are separated by these many nucleotides.
get_FDR	Logical, if FALSE, FDR is not reported.
proximity_assisted	Logical, if TRUE, proximally located regions are tested together.
proximity	Maximum distance between constructed regions for them to be considered proximal.
proximity_defined_length	If performing a "proximity-assisted" test, minimum end-to-end length of a region to be tested.

Value

Constructs regions, reports p-values and FDR for them.

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