RLSeq {RLSeq}R Documentation

RLSeq

Description

Executes the RLSeq analysis workflow.

Usage

RLSeq(object, quiet = FALSE, skip = NULL, ...)

Arguments

object

An RLRanges object.

quiet

If TRUE, messages are suppressed. Default: FALSE.

skip

Analysis steps to skip. Default: NULL. See details for options.

...

Arguments passed to analyzeRLFS.

Details

The RLSeq() function does all of the following by default:

  1. RLFS Perm Test. Runs the analyzeRLFS function to test the enrichment of user-supplied ranges within R-loop-forming sequences. Cannot be skipped.

  2. Predict Condition. Runs the predictCondition function to predict whether the user-supplied sample robustly maps R-loops or not. Cannot be skipped.

  3. Feature enrichment test. Runs the featureEnrich function to test the enrichment of user-supplied ranges within R-loop-relevant genomic features. Skip with skip="featureEnrich".

  4. Correlation Analysis. Runs the corrAnalyze function to test the correlation of user-supplied R-loop signal with other samples in RLBase around "gold-standard" R-loop regions. Skip with skip="corrAnalyze".

  5. Gene annotation. Runs the geneAnnotation function to find the overlap of genes with the user-supplied ranges. Skip with skip="geneAnnotation".

  6. R-loop Region Analysis. Runs the rlRegionTest function to find the overlap of user-supplied ranges with consensus R-loop sites (RL-Regions). Skip with skip="rlRegionTest".

Value

An RLRanges object with results available (see rlresult).

Examples


# Example RLRanges
rlr <- readRDS(system.file("extdata", "rlrsmall.rds", package = "RLSeq"))

# Run RLSeq
# `useMask=FALSE`, `ntime=10`, and `skip=` for demonstration purposes here.
rlr <- RLSeq(
    rlr, useMask = FALSE, ntimes = 10,
    skip=c('featureEnrich', 'corrAnalyze', 'geneAnnotation', 'rlRegionTest')
)


[Package RLSeq version 1.0.0 Index]