plotVmat.GRanges: A function to compute (and plot) a Vmat

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

A function to compute (and plot) a Vmat

Description

The plotVmat.GRanges() method computes and normalizes a Vmat before passing it to plotVmat.Vmat() method.

Usage

## S3 method for class 'GRanges'
plotVmat(
  x,
  granges,
  xlims = c(-250, 250),
  ylims = c(50, 300),
  normFun = "",
  s = 0.95,
  roll = 3,
  cores = 1,
  return_Vmat = FALSE,
  verbose = 1,
  ...
)

Arguments

x	GRanges, paired-end fragments
granges	GRanges, loci to map the fragments onto
xlims	x limits of the computed Vmat
ylims	y limits of the computed Vmat
normFun	character. A Vmat should be scaled either by: 'libdepth+nloci', e.g. the library depth and the number of loci used to compute the Vmat; zscore, if relative patterns of fragment density are more important than density per se; Alternatively, the Vmat can be scaled to a chosen quantile ('quantile') or to the max Vmat value ('max').
s	A float indicating which quantile to use if 'quantile' normalization is chosen
roll	integer, to use as the window to smooth the Vmat rows by rolling mean.
cores	Integer, number of threads to parallelize fragments subsetting
return_Vmat	Boolean, should the function return the computed Vmat rather than the plot?
verbose	Boolean
...	additional parameters

Value

A Vmat ggplot

Examples

data(bam_test)
data(ce11_proms)
V <- plotVmat(
    bam_test,
    ce11_proms,
    normFun = 'libdepth+nloci', 
    roll = 5
)

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