readMSdata: Read raw mass spectral data files.
In hansenlab/yamss: Tools for high-throughput metabolomics

Description Usage Arguments Value Examples

Creates a CMSraw object that contains a data.table of raw mass spectral information for all samples. The resulting object also stores phenotype and sample information. This object is the basic encapsulation of essential raw experimental data and serves as the output for further processing methods.

1	readMSdata(files, colData, mzsubset, verbose)

`files`	A character vector of filenames pointing to the raw data.
`colData`	A `DataFrame` of phenotype and sample information.
`mzsubset`	A length-2 vector indicating a subset of the M/Z range to process. `NULL` otherwise.
`verbose`	Should the function be verbose?

A vector with length equal to the number of scans containing the log2 sum of intensities at each scan.

if (require(mtbls2)) {
data(mtbls2)
filepath <- file.path(find.package("mtbls2"), "mzML")
file <- list.files(filepath, pattern = "MSpos-Ex1",
                   recursive = TRUE, full.names = TRUE)[1]
colData <- DataFrame(group = "wild-type")
cmsRaw <- readMSdata(files = file, colData = colData, verbose = TRUE)
}