ImportFameSettings: Retention time markers settings
In TargetSearch: A package for the analysis of GC-MS metabolite profiling data

Description Usage Arguments Details Value Author(s) See Also Examples

This function imports a list of retention standard markers.

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

`tmp.file`	A character string naming a file with standard markers.
`mass`	The m/z standard marker.
`...`	Other options passed to `read.delim` function.

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.

A tsRim object.

Alvaro Cuadros-Inostroza, Matthew Hannah, Henning Redestig

RIcorrect, tsRim

# 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