normalizeVmat: A function to normalized a Vmat

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

A function to normalized a Vmat

Description

This function normalizes a Vmat. Several different approaches have been implemented to normalize the Vmats.

Usage

normalizeVmat(
  Vmat,
  bam_granges,
  granges,
  normFun = c("zscore"),
  s = 0.99,
  roll = 1,
  verbose = TRUE
)

Arguments

Vmat	A Vmat, usually output of computeVmat
bam_granges	GRanges, the paired-end fragments
granges	GRanges, the regions to map the fragments onto
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.
verbose	Boolean

Value

A normalized Vmat object

Examples

data(bam_test)
data(ce11_all_REs)
Vmat <- computeVmat(bam_test, ce11_all_REs)
Vmat <- normalizeVmat(
    Vmat, 
    bam_test, 
    ce11_all_REs,
    normFun = c('libdepth+nloci')
)

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