Description Usage Arguments Value See Also Examples

Given a set of TCs and genome-wide CTSS coverage, reduce the width of TC until a certain amount of expression has been removed.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 | ```
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`

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 | ```
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))
``` |

MalteThodberg/CAGEfightR documentation built on March 14, 2019, 10:56 p.m.

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