apLCMS.align: apLCMS.align

In yufree/xMSanalyzer: xMSanalyzer: R package for data analysis, comparison, and annotation of metabolomics data.

Description

Call apLCMS function, cdf.to.ftr, at different parameter settings

Usage

apLCMS.align(cdfloc, apLCMS.outloc, min.run.list = c(3, 3), min.pres.list = c(0.3, 
    0.8), minexp = 2, mztol = 1e-05, alignmztol = NA, alignchrtol = NA, numnodes = 2, 
    run.order.file = NA, subs = NA, filepattern = ".cdf", apLCMSmode = "untargeted", 
    known_table, match_tol_ppm = 5)

Arguments

cdfloc	The folder where all NetCDF/mzML/mzXML/mzData files to be processed are located. For example "C:/experiment1/cdf/"
apLCMS.outloc	The folder where alignment output will be written. For example "C:/experiment1/apLCMSoutput/"
min.run.list	List of values for min.run parameter, eg: c(3,6) would run the cdf.to.ftr function at min.run=3 and min.run=6
min.pres.list	List of values min.pres, eg: c(0.3,0.8) would run the cdf.to.ftr function at min.run=3 and min.run=6
minexp	If a feature is to be included in the final feature table, it must be present in at least this number of spectra, eg:2
mztol	The user can provide the m/z tolerance level for peak identification to override the programs selection of the tolerance level. This value is expressed as the percentage of the m/z value. This value, multiplied by the m/z value, becomes the cutoff level. Please see the help for proc.cdf() for details.
alignmztol	The user can provide the m/z tolerance level for peak alignment to override the programs selection. This value is expressed as the percentage of the m/z value. This value, multiplied by the m/z value, becomes the cutoff level.Please see the help for feature.align() for details.
alignchrtol	The retention time tolerance level for peak alignment. The default is NA, which allows the program to search for the tolerance level based on the data. Default: 10
numnodes	Number of nodes to use for processing.
run.order.file	Name of a tab-delimited file that includes sample names sorted by the order in which they were run (sample names must match the CDF file names)
subs	If not all the CDF files in the folder are to be processed, the user can define a subset using this parameter. For example, subs=15:30, or subs=c(2,4,6,8)
filepattern	File format of processed data files. eg: ".cdf", ".mzXML"
apLCMSmode	"untargeted" or "hybrid"; Default: "untargeted"
known_table	A data frame containing the known metabolite ions and previously found features. Please see documentation of semi.sup() function in apLCMS for more details.
match_tol_ppm	The ppm tolerance to match identified features to known metabolites/features. Used by the semi.sup() function in apLCMS. Default: 5

Details

This utility calls the cdf.to.ftr() function in the apLCMS package and performs serial sample processing at multiple combinations of two parameters: min.run (minimum length of elution time for a series of signals grouped by m/z to be considered a feature; default value: 3) and min.pres (minimum proportion of scans in which the signal was present; default values: 0.3, 0.8). The function allows the user to define parameters such as min.exp (minimum number of samples in which a feature is present). This differs from the original apLCMS in that the original only allows one set of parameters, whereas this function allows multiple sets. The resulting tables containing m/z, retention time, and peak intensities in each sample are stored at each parameter combination.

Value

Feature table after weak signal recovery. This is the end product of the function cdf.to.ftr.

Author(s)

Karan Uppal <[e-mail]>

References

http://www.sph.emory.edu/apLCMS/

yufree/xMSanalyzer documentation built on May 4, 2019, 6:35 p.m.