getCombs {dStruct}R Documentation

Identifies subgroupings of replicates for assessing within-group and between-group variation.

Description

Regroup all the samples of A and B groups into homogoneous and heterogeneous sub-groups. Each homogenous sub-group contains replicates of either group A only or group B only. Each heterogeneous sub-group has a mix of samples from both the groups A and B.

Usage

getCombs(
  reps_A,
  reps_B,
  batches = FALSE,
  between_combs = NULL,
  within_combs = NULL
)

Arguments

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.

between_combs

Dataframe with each column containing groupings of replicates of groups A and B, which will be used to assess between-group variation.

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.

Value

List of two dataframes, containing groupings for within-group and between-group variation.

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

#Get heterogeneous and homogeneous set combinations of samples when there are 2 samples of group A and 1 of group B.
getCombs(2, 1)

[Package dStruct version 1.0.0 Index]