analyzeRLFS: Analyze RLFS

In Bishop-Laboratory/RLSeq: RLSeq: An analysis package for R-loop mapping data

Analyze RLFS

Description

Analyzes the enrichment of ranges within R-loop forming sequences (RLFS). See details.

Usage

analyzeRLFS(
  object,
  mask = NULL,
  quiet = FALSE,
  useMask = TRUE,
  noZ = FALSE,
  ntimes = 100,
  stepsize = 50,
  ...
)

Arguments

object	An RLRanges object.
mask	GRanges object containing masked genomic ranges. Not needed unless masked genome unavailable (see genomeMasks). Custom masks can be generated using regioneR::getMask.
quiet	If TRUE, messages are suppressed. Default: FALSE.
useMask	If FALSE, masked genome is not used. This is not recommended unless a mask is unavailable as it can lead to spurious results. Default: TRUE.
noZ	If TRUE, Z-score distribution is not calculated. Default: FALSE.
ntimes	Number of permutations to perform (default: 100).
stepsize	The step size for calculating the Z score distribution. Default: 50. See also regioneR::localZScore.
...	Arguments passed to regioneR::permTest.

Details

R-loop forming sequences are regions of the genome with sequences that are favorable for R-loop formation. They are computationally predicted with the QmRLFS-finder software program and serve as a data-independent test of whether a sample has mapped R-loops robustly or not.

Method

Permutation testing is implemented via regioneR::permTest such that, for each permutation, R-loop peaks were randomized using regioneR::circularRandomizeRegions and then the number of overlaps with RLFS are counted. 100 permutations are used by default to build an empirical distribution for peak/RLFS overlap. Then the true number of overlaps from non-randomized peaks and RLFS are compared to the null distribution to calculate Z-score and significance of enrichment. Finally, a Z-score distribution was calculated (using regioneR::localZScore) 5kb upstream and downstream of the average RLFS midpoint.

These results are subsequently used in the binary classification of the sample as "POS" (maps R-loops) or "NEG" (does not map R-loops). See also predictCondition.

Value

An RLRanges object with RLFS analysis results accessible via RLSeq::rlresult(object, "rlfsRes"). Contains the following structure:

• perTestResults

  • An object of the class permTestResultsList from regioneR with the results of permutation testing. See also regioneR::permTest for full description.

• Z-scores

  • An object of the class localZScoreResultsList from regioneR. Contains the results of local Z-score analysis +/-5kb around each RLFS. See also regioneR::localZScore.

Examples

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

# Perform RLFS analysis (remove ntimes=2 and noZ=TRUE for a typical analysis)
rlr <- analyzeRLFS(rlr, ntimes = 2, noZ = TRUE)

Bishop-Laboratory/RLSeq documentation built on Jan. 28, 2023, 11:38 p.m.