`R/fragsize.R`

`getFragmentsDistribution.Rd`

This function takes fragments and compute the distribution of their sizes over a set or multiple sets of GRanges.

getFragmentsDistribution( fragments, granges_list = NULL, extend_granges = c(-500, 500), limits = c(0, 600), roll = 3, cores = 1 )

fragments | GRanges object containing paired-end fragments. See importPEBamFiles for more details on how to create such object. |
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granges_list | GRanges, can be a list of different sets of GRanges. |

extend_granges | numeric vector of length 2, how the GRanges should be extended. |

limits | numeric vector of length 2, only consider fragments within this window of sizes. |

roll | Integer, apply a moving average of this size |

cores | Integer, number of threads used to compute fragment size distribution |

A list of tbl, one for each .bam file.

data(bam_test) data(ce11_proms) df <- getFragmentsDistribution( bam_test, ce11_proms, extend_granges = c(-500, 500) )#> Warning: NAs introduced by coercion#> Warning: NAs introduced by coercion#> Warning: NAs introduced by coercion#> class x y #> 1 granges 1 NA #> 2 granges 2 0 #> 3 granges 3 0 #> 4 granges 4 0 #> 5 granges 5 0 #> 6 granges 6 0#> [1] 147