specmine (version 1.0)

create_dataset: Create dataset

Description

Create a dataset from existing objects

Usage

create_dataset(datamatrix, type = "undefined", metadata = NULL, 
description = "", sample.names = NULL, x.axis.values = NULL,
label.x = NULL, label.values = NULL, xSet = NULL)

Arguments

datamatrix

matrix with numerical data: rows are assumed to be variables and columns assumed to be samples.

type

type of data: string that can be one of the following:

• nmr-spectra
• nmr-peaks
• ir-spectra
• uvv-spectra
• raman-spectra
• fluor-spectra
• ms-spectra
• lcms-peaks
• gcms-peaks
• integrated-d

metadata

data frame with the dataset's metadata: columns represent each metadata variable and rows represent the value of the metadata for the sample.

description

string with a short description of the dataset.

sample.names

vector with sample names, if NULL then the column names of datamatrix or sequential numbers will be used.

x.axis.values

vector with the x axis values, if NULL then the row names of datamatrix or sequential numbers will be used.

label.x

x axis label.

label.values

values label.

xSet

xcmsSet object from xcms package to store the reading and preprocessing results from MS spectra. Used for metabolite identification purposes.

Value

• list representing the dataset:
• data
  matrix with the data
• type
  type of the data
• description
  short description of the dataset
• metadata
  data frame with the metadata variables
• labels
  list with labels of x axis and values
• xSet
  xcmsSet object

Examples

## Example of creating a dataset
  dataset = create_dataset(datamatrix, type = "nmr-spectra", 
	metadata = dataset.metadata, description = "shortdescription", 
	sample.names = NULL, x.axis.values = NULL, label.x = "ppm", 
	label.values = "intensity")