dStructGuided {dStruct}R Documentation

Performs guided discovery of differentially reactive regions.

Description

This function takes as input reactivity profiles for a transcript region from samples of two groups. First, it regroups the samples into homogeneous and heteregenous sub-groups, which are used to compute the within-group and between-group nucleotide-wise d scores. If the region meets the quality criteria, the between- and within-group d scores are compared using the Wilcoxon signed-rank test. The resulting p-values quantify the significance of difference in reactivity patterns between the two input groups.

Usage

dStructGuided(
  rdf,
  reps_A,
  reps_B,
  batches = FALSE,
  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) and the median of nucleotide-wise difference of between-group and within-group d-scores.

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.

Examples

#Load Wan et al., 2014 data
data(wan2014)

#Run dStruct in the guided mode on first region in wan2014.
dStructGuided(wan2014[[1]], reps_A = 2, reps_B = 1)

[Package dStruct version 0.99.3 Index]