normalize_data: Normalizing log data

In hyochoi/SCISSOR: Shape changes in selecting sample outliers in RNA-seq

Normalizing log data

Description

This function reduces the variation associated with sequencing depths remaining after a log transformation. The output is the main data object for the downstream shape change detection miscGlobal.

Usage

normalize_data(
  inputData,
  pileupData,
  Ranges,
  smoothness = 0.7,
  makePlot = FALSE,
  ...
)

Arguments

inputData	log-transformed data matrix (e.g. object from logtransform_data)
pileupData	raw coverage data matrix
makePlot	logical, whether to plot variation with respect to overall expression with fitted curve. Default is FALSE
exonset	exon/intron annotation matrix from process_data
Gene	gene name to print in the plot

hyochoi/SCISSOR documentation built on July 6, 2022, 6:59 a.m.