specmine (version 1.0)

read_ms_spectra: Read MS spectra

Description

Read the data from the MS files and creates the dataset.

Usage

read_ms_spectra(folder.name, type = "undefined", 
filename.meta = NULL, description = "", prof.method = "bin", 
fwhm = 30, bw = 30, intvalue = "into", header.col.meta = TRUE, 
header.row.meta = TRUE, sep.meta = ",")

Arguments

folder.name

string containing the path of the data folder.

type

type of the data.

filename.meta

name of the metadata file.

description

a short text describing the dataset.

prof.method

profmethod parameter from xcmsSet function from xcms package.

fwhm

fwhm parameter from xcmsSet function from xcms package. A commonly used value is 30 (seconds) for LC-MS and 4 (seconds) for GC-MS spectra.

bw

bw parameter from group function from xcms package.

intvalue

value parameter from groupval function from xcms package. It can be:

• "into" - integrated area of original (raw) peak
• "intf" - integrated area of filtered peak.
• "maxo" - maximum intensity of original (raw) peak.
• "maxf" - maximum intensity of filtered peak.

header.col.meta

boolean value indicating if the metadata CSV file contains a header column with the name of the metadata variables.

header.row.meta

boolean value indicating if the metadata CSV file contains a header row with the name of the samples.

sep.meta

the separator character of the metadata file.

Value

Returns a dataset from the MS files.

Examples

## Not run: 
#   ## Example of reading a dataset from MS files
#   dataset = read_ms_spectra("data", type = "nmr-spectra", "metadata.csv", 
# 	    description = "description of the dataset")
# ## End(Not run)