dStruct.guided: Performs guided discovery of differentially reactive regions.

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

Description

Performs guided discovery of differentially reactive regions.

Usage

dStruct.guided(rdf, reps_A, reps_B, batches = F, within_combs = NULL,
  between_combs = NULL, check_quality = TRUE, quality = "auto",
  evidence = 0)

Arguments

rdf	Dataframe of reactivities for each sample. Each column must be labelled as A1, A2, ..., B1, B2, ...
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.
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.
check_quality	Logical, if TRUE, check 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.

Value

p-value for the tested region, estimated using one-sided Wilcoxon signed rank test.

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