A function to compute sizes distribution for PE fragments

A function to compute sizes distribution for PE fragments

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

Arguments

fragments

GRanges object containing PE fragments. See importPEBamFiles for more details.
extend_granges

A numeric vector of length 2. How the GRanges should be extended.
limits

A numeric vector of length 2. Only consider fragments within this window of sizes.
roll

Integer Apply a moving average of this size
granges

GRanges. cam be a list of different sets of GRanges. should overlap in order to be considered when estimating fragment sizes.

Value

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