dCombs {dStruct}R Documentation

Assesses within-group or between-group variation.

Description

Given the reactivity profiles for a transcript from multiple samples, and a list of sample identifiers, this function computes the dissimilarity of reactivity scores between the specified samples. These are returned as a sequence of nucleotide-wise d scores.

Usage

dCombs(rdf, combs)

Arguments

rdf

Data.frame of reactivities for each sample.

combs

Data.frame with each column containing groupings of samples.

Value

Nucleotide-wise 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

#Example of a data frame with reactivities.
reacs <- data.frame(matrix(runif(30, 0, 10), 10, 3))

#The columns of data frame with must indicate sample grouping and id.
colnames(reacs) <- c("A1", "A2", "B1")

#Get nucleotide-wise dissimilarity scores for a set of samples.
dCombs(rdf = reacs, combs = data.frame(c("A1", "B1")))

[Package dStruct version 1.0.0 Index]