BSFind: RBP binding site definition for iCLIP data

In ZarnackGroup/BindingSiteFinder: Binding site defintion based on iCLIP data

RBP binding site definition for iCLIP data

Description

This is the main function that performs the binding site definition analysis through the following steps:

1. Filter PureCLIP sites by their score distribution: pureClipGlobalFilter

2. Estimate the appropriate binding site width together with the optimal gene-wise filter level: estimateBsWidth

3. Filter PureCLIP sites by their score distribution per gene: pureClipGeneWiseFilter

4. Define equally sized binding sites: makeBindingSites

5. Perform replicate reproducibility filter: reproducibilityFilter

6. Assign binding sites to their hosting genes: assignToGenes

7. Assign binding sites to their hosting transcript regions: assignToTranscriptRegions

8. Re-assign PureCLIP scores to binding sites: annotateWithScore

9. Calculation of signal-to-flank ratio: calculateSignalToFlankScore

Usage

BSFind(
  object,
  bsSize = NULL,
  cutoff.geneWiseFilter = NULL,
  cutoff.globalFilter = 0.01,
  est.bsResolution = "medium",
  est.geneResolution = "medium",
  est.maxBsWidth = 13,
  est.minimumStepGain = 0.02,
  est.maxSites = Inf,
  est.subsetChromosome = "chr1",
  est.minWidth = 2,
  est.offset = 1,
  est.sensitive = FALSE,
  est.sensitive.size = 5,
  est.sensitive.minWidth = 2,
  merge.minWidth = 2,
  merge.minCrosslinks = 2,
  merge.minClSites = 1,
  merge.CenterIsClSite = TRUE,
  merge.CenterIsSummit = TRUE,
  repro.cutoff = NULL,
  repro.nReps = NULL,
  repro.minCrosslinks = 1,
  overlaps.geneWiseFilter = "keepSingle",
  overlaps.geneAssignment = "frequency",
  overlaps.rule.geneAssignment = NULL,
  overlaps.TranscriptRegions = "frequency",
  overlaps.rule.TranscriptRegions = NULL,
  stf.flank = "bs",
  stf.flank.size = NULL,
  match.score = "score",
  match.geneID = "gene_id",
  match.geneName = "gene_name",
  match.geneType = "gene_type",
  match.ranges.score = NULL,
  match.option.score = "max",
  anno.annoDB = NULL,
  anno.genes = NULL,
  anno.transcriptRegionList = NULL,
  quiet = FALSE,
  veryQuiet = FALSE,
  ...
)

Arguments

object	a BSFDataSet object with stored ranges
bsSize	an odd integer value specifying the size of the output binding sites
cutoff.geneWiseFilter	numeric; defines the cutoff for which sites to remove in in function pureClipGeneWiseFilter. The smallest step is 1% (0.01). A cutoff of 5% will remove the lowest 5% sites, given their score, on each gene, thus keeping the strongest 95%.
cutoff.globalFilter	numeric; defines the cutoff for which sites to keep, the smallest step is 1% (0.01) in function pureClipGlobalFilter
est.bsResolution	character; level of resolution of the binding site width in function estimateBsWidth
est.geneResolution	character; level of resolution of the gene-wise filtering in function estimateBsWidth
est.maxBsWidth	numeric; the largest binding site width which should considered in the testing
est.minimumStepGain	numeric; the minimum additional gain in the score in percent the next binding site width has to have, to be selected as best option
est.maxSites	numeric; maximum number of PureCLIP sites that are used
est.subsetChromosome	character; define on which chromosome the estimation should be done in function estimateBsWidth
est.minWidth	the minimum size of regions that are subjected to the iterative merging routine, after the initial region concatenation.
est.offset	constant added to the flanking count in the signal-to-flank ratio calculation to avoid division by Zero
est.sensitive	logical; whether to enable sensitive pre-filtering before binding site merging or not
est.sensitive.size	numeric; the size (in nucleotides) of the merged sensitive region
est.sensitive.minWidth	numeric; the minimum size (in nucleoties) of the merged sensitive region
merge.minWidth	the minimum size of regions that are subjected to the iterative merging routine, after the initial region concatenation.
merge.minCrosslinks	the minimal number of positions to overlap with at least one crosslink event in the final binding sites
merge.minClSites	the minimal number of crosslink sites that have to overlap a final binding site
merge.CenterIsClSite	logical, whether the center of a final binding site must be covered by an initial crosslink site
merge.CenterIsSummit	logical, whether the center of a final binding site must exhibit the highest number of crosslink events
repro.cutoff	numeric; percentage cutoff to be used for the reproducibility quantile filtering
repro.nReps	numeric; number of replicates that must meet the cutoff defined in repro.cutoff for a binding site to be called reproducible. Defaults to N-1.
repro.minCrosslinks	numeric; minimal number of crosslinks a binding site needs to have to be called reproducible. Acts as a lower boundary for repro.cutoff. Defaults to 1.
overlaps.geneWiseFilter	character; how overlaps should be handled in pureClipGeneWiseFilter
overlaps.geneAssignment	character; how overlaps should be handled in assignToGenes
overlaps.rule.geneAssignment	character vector; a vector of gene types that should be used to handle overlaps if option 'hierarchy' is selected for assignToGenes. The order of the vector is the order of the hierarchy.
overlaps.TranscriptRegions	character; how overlaps should be handled in assignToTranscriptRegions
overlaps.rule.TranscriptRegions	character vector; a vector of gene types that should be used to handle overlaps if option 'hierarchy' is selected for assignToTranscriptRegions. The order of the vector is the order of the hierarchy.
stf.flank	character; how the flanking region shoule be set. Options are 'bs', 'manual'
stf.flank.size	numeric; if flank='manual' provide the desired flanking size
match.score	character; meta column name of the crosslink site
match.geneID	character; meta column name of the genes
match.geneName	character; meta column name of the gene name
match.geneType	character; meta column name of the gene type
match.ranges.score	a GRanges object, with numeric column for the score to match in function annotateWithScore
match.option.score	character; meta column name of the crosslink site in function annotateWithScore
anno.annoDB	an object of class OrganismDbi that contains the gene annotation !!! Experimental !!!
anno.genes	an object of class GenomicRanges that represents the gene ranges directly
anno.transcriptRegionList	an object of class CompressedGRangesList that holds an ranges for each transcript region
quiet	logical; whether to print messages
veryQuiet	logical; whether to suppress all messages
...	additional arguments passed to estimateBsWidth, makeBindingSites and reproducibilityFilter

Details

If only the annotation is provided (anno.genes and anno.transcriptRegionList), then binding sites size (bsSize) and gene-wise cutoff (cutoff.geneWiseFilter) are estimated using estimateBsWidth. To avoid this behavior one has to provide input values for the arguments bsSize and cutoff.geneWiseFilter.

If no binding site size is provided through bsSize, then estimateBsWidth is called to estimate the optimal size for the given data-set. The result of this estimation can be looked at with estimateBsWidthPlot and arguments can be adjusted if needed.

Use the processingStepsFlowChart function to get an overview of all steps carried out by the function.

For complete details on each step, see the manual pages of the respective functions. The BSFind function returns a BSFDataSet with ranges merged into binding sites. A full flowchart for the entire process can be visualized with processingStepsFlowChart. For each of the individual steps dedicated diagnostic plots exists. Further information can be found in our Bioconductor vignette: https://www.bioconductor.org/packages/release/bioc/html/BindingSiteFinder.html

Value

an object of class BSFDataSet with ranges merged into binding sites given the inputs.

See Also

BSFDataSet, estimateBsWidth, pureClipGlobalFilter, pureClipGeneWiseFilter, assignToGenes, assignToTranscriptRegions, annotateWithScore, reproducibilityFilter, calculateSignalToFlankScore, processingStepsFlowChart

Examples

# load clip data
files <- system.file("extdata", package="BindingSiteFinder")
load(list.files(files, pattern = ".rda$", full.names = TRUE))
# Load genes
load(list.files(files, pattern = ".rds$", full.names = TRUE)[1])
# load transcript regions
load(list.files(files, pattern = ".rds$", full.names = TRUE)[2])
BSFind(object = bds, bsSize = 9, anno.genes = gns,
 anno.transcriptRegionList = regions, est.subsetChromosome = "chr22")

ZarnackGroup/BindingSiteFinder documentation built on May 31, 2024, 3:29 a.m.