ImportSamples {TargetSearch} | R Documentation

## Sample definitions

### Description

This function imports a sample list that will be processed from a tab delimited file.

### Usage

    ImportSamples(sampfile, CDFpath=".", RIpath=".", ftype=c("binary", "text"), ...)

    ImportSamplesFromDir(CDFpath=".", RIfiles=FALSE, ignore.case=TRUE,
    	ftype=c("binary", "text"))

### Arguments

`sampfile` | A character string naming a sample file or a `data.frame` See details.
`CDFpath` | A character string naming a directory where the CDF files are located.
`RIpath` | A character string naming a directory where the RI corrected text files are/will be located.
`RIfiles` | Logical. If `TRUE`, the function will look for for RI files (RI_*) instead of CDF files (the default).
`ftype` | A character string giving the file type for RI files. Options are "binary" and "text".
`ignore.case` | Logical. Should pattern-matching be case-insensitive?
`...` | Other options passed to `read.delim` function.

### Details

The sample file is a tab-delimited text file or, alternatively, a `data.frame` like the one would get by calling `read.delim`. The following two columns are expected:

- `CDF_FILE` - The list of baseline corrected CDF files.

- `MEASUREMENT_DAY` - The day when the sample was measured.

The function first looks for columns matching those names. If they are not found, then it looks for columns with the substrings 'cdf' and 'day' respectively. If the 'cdf' column is not found, the function raises an error, but if 'day' is not found, then it assumes the measurement day is the same for all. In case of multiple matches, then it takes the first column. The column order does not matter. Other columns could be included in that file. They won't be used by the script, but will be included in the "sample" R object.

The `ftype` parameter sets the file format of the RI files, which are created by the function `RIcorrect`. "text" is the classic text format and "binary" is a binary version, designed for speed, of the text format (TargetSearch >= 1.12.0). The file format can be identified by the file extension (".txt" for text, ".dat" for binary), but this is just an indicator: the file format is detected dinamically during file reading. Use the method `fileFormat` to set or get this parameter.

### Value

A `tsSample` object.

### Author(s)

Alvaro Cuadros-Inostroza, Matthew Hannah, Henning Redestig

### See Also

`ImportLibrary`, `tsSample`

### Examples

    # get the sample definition definition file
    cdfpath <- file.path(find.package("TargetSearchData"), "gc-ms-data")
    sample.file  <- file.path(cdfpath, "samples.txt")

    # set a path where the RI files will be created
    RIpath <- "."

    # import samples
    sampleDescription <- ImportSamples(sample.file, CDFpath = cdfpath, RIpath = RIpath)

    # change the sample names. It is required that the names must be unique.
    sampleNames(sampleDescription) <- paste("Sample", 1:length(sampleDescription), sep = "_")

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

[Package TargetSearch version 1.40.3 Index]