getFragmentsDistribution: A function to compute sizes distribution for paired-end...

In js2264/VplotR: Set of tools to make V-plots and compute footprint profiles

A function to compute sizes distribution for paired-end fragments

Description

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

Usage

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

Arguments

fragments	GRanges object containing paired-end fragments. See importPEBamFiles for more details on how to create such object.
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

Value

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

Examples

data(bam_test)
data(ce11_proms)
df <- getFragmentsDistribution(
    bam_test, 
    ce11_proms,
    extend_granges = c(-500, 500)
)
head(df)
which.max(df$y)

js2264/VplotR documentation built on Jan. 4, 2024, 7:49 p.m.