trimToPercentiles {CAGEfightR} | R Documentation |
Given a set of TCs and genome-wide CTSS coverage, reduce the width of TC until a certain amount of expression has been removed.
trimToPercentiles(object, pooled, ...) ## S4 method for signature 'GRanges,GRanges' trimToPercentiles(object, pooled, percentile = 0.1, symmetric = FALSE) ## S4 method for signature 'GRanges,GPos' trimToPercentiles(object, pooled, ...) ## S4 method for signature 'RangedSummarizedExperiment,GenomicRanges' trimToPercentiles(object, pooled, ...) ## S4 method for signature 'GRanges,RangedSummarizedExperiment' trimToPercentiles(object, pooled, ...) ## S4 method for signature ## 'RangedSummarizedExperiment,RangedSummarizedExperiment' trimToPercentiles(object, pooled, ...)
object |
GenomicRanges or RangedSummarizedExperiment: TCs to be trimmed. |
pooled |
GenomicRanges or RangedSummarizedExperiment: CTSS coverage. |
... |
additional arguments passed to methods. |
percentile |
numeric: Fraction of expression to remove from TCs. |
symmetric |
logical: Whether to trim the same amount from both edges of the TC (TRUE) or always trim from the least expressed end (FALSE). |
GRanges with trimmed TCs, including recalculated peaks and scores.
Other Clustering functions:
clusterBidirectionally()
,
clusterUnidirectionally()
,
trimToPeak()
,
tuneTagClustering()
Other Trimming functions:
trimToPeak()
data(exampleCTSSs) data(exampleBidirectional) # Calculate pooled CTSSs exampleCTSSs <- calcTPM(exampleCTSSs, totalTags='totalTags') exampleCTSSs <- calcPooled(exampleCTSSs) # Choose a few wide clusters: TCs <- subset(exampleUnidirectional, width >= 100) # Symmetric trimming (same percentage from each side): TCs_sym <- trimToPercentiles(TCs, pooled=exampleCTSSs, symmetric=FALSE) # Assymmetric trimming (always trim from lowest side): TCs_asym <- trimToPercentiles(TCs, pooled=exampleCTSSs, symmetric=TRUE) # Compare the two results sets of widths: summary(width(TCs_sym) - width(TCs_asym))