RLSeq {RLSeq} | R Documentation |
Executes the RLSeq analysis workflow.
RLSeq(object, quiet = FALSE, skip = NULL, ...)
object |
An RLRanges object. |
quiet |
If |
skip |
Analysis steps to skip.
Default: |
... |
Arguments passed to analyzeRLFS. |
The RLSeq()
function does all of the following by default:
RLFS Perm Test. Runs the analyzeRLFS function to test the enrichment of user-supplied ranges within R-loop-forming sequences. Cannot be skipped.
Predict Condition. Runs the predictCondition function to predict whether the user-supplied sample robustly maps R-loops or not. Cannot be skipped.
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"
.
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"
.
Gene annotation. Runs the geneAnnotation function to find the overlap
of genes with the user-supplied ranges. Skip with skip="geneAnnotation"
.
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"
.
An RLRanges object with results available (see rlresult).
# 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') )