PreprocessData: Generate MA plots of raw and normalized data

In TomNash/NASHMAP: Microarray Analysis Pipeline

Description

Normalize input raw data using quantile and mloess methods. Plots of the normalized data along with a dendrogram clustering all samples will be stored in newly created pipeline directory.

Usage

preprocessPlots(input.file, file.sheet=1, ntext=2, data.col, 
symbol.index=1, id.index=2)

Arguments

input.file	Path to the microarray expression file, be it .xlsx or .csv
file.sheet	Sheet number in the spreadsheet with data
ntext	Number of leading text columns
data.col	Range of columns which contain data (indexing begins with first column of file)
symbol.index	Column index which contains gene symbols
id.index	Column index which contains gene ID's
batch.vector	Character vector indicating to which batch each sample belongs

Value

A list with components

ntext	Number of leading text columns
data.col	Vector of column indices containing array data
id	Vector containing gene ID's
id.index	Column index containing gene ID information
symbol	Vector containing gene symbols
symbol.index	Column index containing gene symbol information
desc.stats	Vector of column indices containing descriptive statistics
pipeline.name	Name of pipeline generated from input file name sans extension
mloess	Data rame of quantile normalized data
quantile	Data rame of quantile normalized data

TomNash/NASHMAP documentation built on May 9, 2019, 4:54 p.m.