Description Usage Arguments Value See Also Examples

View source: R/hiReadsProcessor.R

Given a group of discrete factors (i.e. position ids) and integer values, the function tests if they overlap between groups. If overlap is found, then the group having highest frequency of a given position wins, else the position is filtered out from all the groups. The main use of this function is to remove crossover sites from different samples in the data.

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`posID` |
a vector of groupings for the value parameter (i.e. Chr,strand). Required if psl.rd parameter is not defined. |

`value` |
a vector of integer locations/positions that needs to be binned, i.e. genomic location. Required if psl.rd parameter is not defined. |

`grouping` |
additional vector of grouping of length posID or psl.rd by which to pool the rows (i.e. samplenames). Default is NULL. |

`weight` |
a numeric vector of weights to use when calculating frequency of value by posID and grouping if specified. Default is NULL. |

`windowSize` |
size of window within which values should be checked. Default is 1. |

`psl.rd` |
a GRanges object. Default is NULL. |

a data frame of the original input with columns denoting whether a given row was a Candidate and isCrossover. If psl.rd parameter is defined, then a GRanges object with 'isCrossover', 'Candidate', and 'FoundIn' columns appended at the end.

`clusterSites`

, `otuSites`

,
`findIntegrations`

, `getIntegrationSites`

,
`pslToRangedObject`

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