| tsSample-class {TargetSearch} | R Documentation |
This is a class to represent a set of samples.
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])
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.[signature(x = "tsSample"): Selects a subset of samples.$namesignature(x = "tsSample"): Access column name of sampleData slot.CDFfilessignature(obj = "tsSample"): list of CDF files. RIfilessignature(obj = "tsSample"): list of RI files. RIpathsignature(obj = "tsSample"): The RI file path. CDFpathsignature(obj = "tsSample"): The CDF file path. lengthsignature(x = "tsSample"): number of samples.sampleDatasignature(obj = "tsSample"): additiona sample information. sampleDayssignature(obj = "tsSample"): measurement days. sampleNamessignature(obj = "tsSample"): sample names.showsignature(object = "tsSample"): the show funtion. Alvaro Cuadros-Inostroza, Matthew Hannah, Henning Redestig
showClass("tsSample")
# get a list of CDF files from a directory
require(TargetSearchData)
CDFpath <- system.file("gc-ms-data", package = "TargetSearchData")
cdffiles <- dir(CDFpath, "cdf")
# define the RI files and the RI path
RIfiles <- sub("cdf$", "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/"