ImportLibrary: Library import

View source: R/ImportLibrary.R

ImportLibraryR Documentation

Library import

Description

These functions import a metabolite library file that will be used to processed the GC-MS data. Two file formats are supported: a tab-delimited format and the more common NIST MSP format.

Usage

ImportLibrary(x, type = c("auto", "tab", "msp"), ...)

ImportLibrary.tab(libfile, fields = NULL, RI_dev = c(2000,1000,200),
    SelMasses = 5, TopMasses = 15, ExcludeMasses = NULL,
    libdata, file.opt=NULL)

ImportLibrary.msp(libfile, fields = NULL, RI_dev = c(2000,1000,200),
    SelMasses = 5, TopMasses = 15, ExcludeMasses = NULL)

Arguments

x

A character string or a data.frame. If data.frame, it will be passed to ImportLibrary.tab as parameter libdata. If character, it will be passed as libfile to either ImportLibrary.tab or ImportLibrary.msp according to the file type (option type).

libfile

A character string naming a library file. See details.

type

The library file format. Possible options are "tab" for a tab-delimited file, "msp" for NIST MSP format, or "auto" for autodetection. Default to "auto".

fields

A two component list. Each component contains a regular expression used to parse and extract the fields for retention index and selection masses. Only meaningful for MSP format.

RI_dev

A three component vector with RI windows.

SelMasses

The number of selective masses that will be used.

TopMasses

The number of most intensive masses that will be taken from the spectrum, if no TOP_MASS is provided.

ExcludeMasses

Optional. A vector containing a list of masses that will be excluded.

libdata

Optional. A data frame with library data. The format is the same as the library file. It is equivalent to importing the library file first with read.table and calling ImportLibrary.tab after. This might be preferable for "fine tuning", for example, if the library file is in CSV format instead of tab-delimited.

file.opt

Optional. A list containing arguments to be passed to read.table.

...

Further arguments passed to ImportLibrary.tab or ImportLibrary.msp

Details

ImportLibrary is a wrapper for functions ImportLibrary.tab and ImportLibrary.msp which detects automatically which function should be called.

ImportLibrary.tab reads a tab delimited text file by calling the function read.table which will be parsed and converted to a tsLib object. The following arguments are used by default (which are not exactly the defaults for read.table):

header=TRUE, sep="\t", quote="", dec=".", fill=TRUE, comment.char="#"

The argument file.opt can be used to change these options. Other alternative is to import first the file with read.table and friends, and call ImportLibrary with the resulting data.frame. This allows more flexibility with libraries with unusual characters, for example.

These columns are needed:

  • libID - A unique identifier for the metabolite.

  • Name - The metabolite name.

  • RI - The expected RI.

  • SEL_MASS - A list of selective masses separated with semicolon.

  • TOP_MASS - A list of the most abundant masses to be searched, separated with semicolons.

  • Win_k - The RI windows, k = 1,2,3. Mass search is performed in three steps. A RI window required for each one of them.

  • SPECTRUM - The metabolite spectrum. m/z and intensity values are separated by spaces, colons or semicolons (see notes on the format below).

  • QUANT_MASS - A list of masses that might be used for quantification. One value per metabolite and it must be one of the selective masses. (optional)

The columns Name and RI are mandatory. At least one of columns SEL_MASS, TOP_MASS and SPECTRUM must be given as well. By using the parameters SelMasses or TopMasses it is possible to set the selective masses or the top masses from the spectra. The parameter ExcludeMasses is used only when masses are obtained from the spectra. The parameter RI_dev can be used to set the RI windows. Note that in this case, all metabolites would have the same RI windows.

The SPECTRUM format can be a list of m/z-intensity pairs separated by colons: 85:8 86:13 87:5 88:4 ..., or similar to the MSP spectrum format (shown below): 85 8; 86 13; 87 5; 88 4; .... The internal parser is not strict, so even a list of integers separated by spaces is allowed, for example, 86 8 86 13 .... The only restriction is that the number of integers is even, otherwise the input is truncated. If the spectrum is not available for some analytes, simply leave the respective cell empty or use NA. Note: Only digits(0-9), spaces, colons(:) and semicolons(;) are allowed in this column; the presence of other characters will generate and error, unless it is NA.

A unique identifier may be provided as well (libID). This could be a external database identifier. If it is not provided, a random identifier will be created of the form GC.k, k = 1,...,N.

The MSP format is a text file that can be imported/exported from NIST. A typical MSP file looks like this:

Name: Pyruvic Acid
Synon: Propanoic acid, 2-(methoxyimino)-, trimethylsilyl ester
Synon: RI: 223090
Synon: SEL MASS: 89|115|158|174|189
Formula: C7H15NO3Si
MW: 189
Num Peaks: 41
  85    8;  86   13;  87    5;  88    4;  89  649;
  90   55;  91   28;  92    1;  98   13;  99  257;
 100  169; 101   30; 102    7; 103   13; 104    1;
 113    3; 114   35; 115  358; 116   44; 117   73;
 118   10; 119    4; 128    2; 129    1; 130   10;
 131    3; 142    1; 143   19; 144    4; 145    1;
 157    1; 158   69; 159   22; 160    4; 173    1;
 174  999; 175  115; 176   40; 177    2; 189   16;
 190    2;

Name: another metabolite
...

Different entries must be separated by empty lines. In order to parse the retention time index (RI) and selective masses (SEL MASS), a two component list containing the field names of RI and SEL_MASS must be provided by using the parameter fields. In this example, use field = list("RI: ", "SEL MASS: "). Note that ImportLibrary expects to find those fields next to "Synon:". Alternatively, you could provide the RI and SEL_MASS using the tsLib methods.

Libraries for TargetSearch and for different retention index systems, such as VAR5 or MDN35, can be downloaded from http://gmd.mpimp-golm.mpg.de/.

Value

A tsLib object.

Author(s)

Alvaro Cuadros-Inostroza, Matthew Hannah, Henning Redestig

See Also

ImportSamples, tsLib

Examples

# get the reference library file
require(TargetSearchData)
lib.file  <- tsd_file_path("library.txt")

# Import the reference library
refLibrary <- ImportLibrary(lib.file)

# set new names for the first 3 metabolites
libName(refLibrary)[1:3] <- c("Metab01", "Metab02", "Metab03")

# change the retention time deviations of Metabolite 3
RIdev(refLibrary)[3,] <- c(3000,1500,150)


acinostroza/TargetSearch documentation built on June 14, 2024, 8:03 a.m.