tsSample-class {TargetSearch}R Documentation

Class for representing samples

Description

This is a class to represent a set of samples.

Objects from the Class

Objects can be created by the function ImportSamples or by calling the object generator function.

new("tsSample", Names = [sample names], CDFfiles = [list of CDF file names], RIfiles = [list of RI file names], CDFpath = [CDF files path], RIpath = [RI files path], days = [measurement days], data = [additional sample information])

Slots

Names:
"character", the sample names.
CDFfiles:
"character", the list of CDF file names.
RIfiles:
"character", the list of RI file names.
CDFpath:
"character", CDF files path.
RIpath:
"character", RI file path.
days:
"character", measurement days.
data:
"data.frame", additional sample information.

Methods

[
signature(x = "tsSample"): Selects a subset of samples.
$name
signature(x = "tsSample"): Access column name of sampleData slot.
CDFfiles
signature(obj = "tsSample"): list of CDF files.
RIfiles
signature(obj = "tsSample"): list of RI files.
RIpath
signature(obj = "tsSample"): The RI file path.
CDFpath
signature(obj = "tsSample"): The CDF file path.
length
signature(x = "tsSample"): number of samples.
sampleData
signature(obj = "tsSample"): additiona sample information.
sampleDays
signature(obj = "tsSample"): measurement days.
sampleNames
signature(obj = "tsSample"): sample names.
show
signature(object = "tsSample"): the show funtion.

Author(s)

Alvaro Cuadros-Inostroza, Matthew Hannah, Henning Redestig

See Also

ImportSamples

Examples

showClass("tsSample")

# get a list of CDF files from a directory
require(TargetSearchData)
CDFpath <- system.file("gc-ms-data", package = "TargetSearchData")
cdffiles <- dir(CDFpath, "cdf")

# define the RI files and the RI path
RIfiles <- sub("cdf$", "txt", paste("RI_", cdffiles, sep = ""))
RIpath  <- "."

# get the measurement days (the four first numbers of the cdf files, in this
# example)
days <- substring(cdffiles, 1, 4)

# sample names 
smp_names <- sub("\.cdf", "", cdffiles)

# add some sample info
smp_data <- data.frame(CDF_FILE =cdffiles, GROUP = gl(5,3))

# create the sample object
sampleDescription <- new("tsSample", Names = smp_names, CDFfiles = cdffiles, CDFpath = CDFpath,
    RIpath = RIpath, days = days, RIfiles = RIfiles, data = smp_data)

# changing the sample names
sampleNames(sampleDescription) <- paste("Sample", 1:length(sampleDescription), sep = "_")

# changing the file paths (relative to the working path)
CDFpath(sampleDescription) <- "my_cdfs/"
RIpath(sampleDescription)  <- "my_RIs/"


[Package TargetSearch version 1.0.0 Index]