dStructome: Performs de novo discovery of differentially reactive regions...

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

Description

Performs de novo discovery of differentially reactive regions for transcriptome-wide data.

Usage

dStructome(rl, 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,
  processes = "auto", method = "denovo", proximity_assisted = F,
  proximity = 10, proximity_defined_length = 30)

Arguments

rl	List of dataframes 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.
processes	Number of parallel processes to use.
method	Character specifying either guided or de novo discovery approach.
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.