ImportLibrary: Library import
In acinostroza/TargetSearch: A package for the analysis of GC-MS metabolite profiling data
View source: R/ImportLibrary.R
ImportLibrary R 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 Nov. 13, 2024, 12:28 a.m.
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View source: R/ImportLibrary.R
| ImportLibrary | R 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 |
libfile |
A character string naming a library file. See details. |
type |
The library file format. Possible options are |
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 |
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 |
file.opt |
Optional. A list containing arguments to be passed to
|
... |
Further arguments passed to |
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)
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