Retention time markers settings

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Description

This function imports a list of retention standard markers.

Usage

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ImportFameSettings(tmp.file = NA, mass = NA, ...)

Arguments

tmp.file

A character string naming a file with standard markers.

mass

The m/z standard marker.

...

Other options passed to read.delim function.

Details

The standard marker file is a tab-delimited text file with 3 or 4 columns. Column names doesn't matter. They must be in the following order.

  • LowerLimit - The Retention time lower limit in seconds.

  • UpperLimit - The Retention time upper limit in seconds.

  • RIstandard - The RI value of that standard.

  • mass - The m/z standard marker. This column is optional since it could be set by the mass parameter.

If no arguments are given, a default object will be returned.

Value

A tsRim object.

Author(s)

Alvaro Cuadros-Inostroza, Matthew Hannah, Henning Redestig

See Also

RIcorrect, tsRim

Examples

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# get the RI marker definition file
cdfpath  <- file.path(find.package("TargetSearchData"), "gc-ms-data")
rim.file <- file.path(cdfpath, "rimLimits.txt")

# set the mass marker to 87
mass <- 87

# load the definition
rimLimits <- ImportFameSettings(rim.file, mass = mass)

# sometimes you need to change the limits of a particular standard
rimLimits(rimLimits)[2,] <- c(410, 450)

# to change the mass value
rimMass(rimLimits) <- 85

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