fileHTS {imageHTS} | R Documentation

## Get access to screen data files

### Description

`fileHTS` builds the path or URL pointing to a screen data file. `readHTS` reads the file pointed by `fileHTS`.

### Usage

      fileHTS(x, type, ..., createPath=FALSE, access='cache')
      readHTS(x, type, ..., access='cache', format=NULL)

### Arguments

`x` | An imageHTS object.
`type` | A character vector, indicating the requested file type. See Details.
`...` | Optional arguments. See Details.
`createPath` | A logical value specifying if the directories along the path should be created. Default is `FALSE`.
`access` | A character string indicating how to access the data. Valid values are `cache` (the default), `local` and `server`. See Details.
`format` | An optional character string indicating the format of the designated file. Valid formats are `tab`, a tab-separated file with headers; `rda`, a R data file; `dcf`, an imageHTS DCF configuration file.

### Details

In imageHTS, all screen data files are accessed through the function `fileHTS`. Screen data can be accessed at two locations: the `localPath`, which is local writable directory, and `serverURL`, which is a server URL. `localPath` and `serverURL` are set during the instantiation of the `imageHTS` object with `parseImageConf`.

If `access` equals `local`, `fileHTS` returns a local path pointing to the requested file. If `server`, `fileHTS` returns a server URL pointing to the requested file. If `cache` (the default), `fileHTS` tests if the file is present at the local path. If not, `fileHTS` tries to download the file from the server and copies it in the local path. `fileHTS` always returns a local path if `access` equals `cache`.

A file is designated by its `type` and optional arguments. Known file types are:

- `file`: general-purpose file. The character string `filename` indicates its path, relative to the project directory. File format is unspecified.

- `source`: source image, designated by the character string `uname` and the numeric `channel`. File format is unspecified.

- `cal`: calibrated image, designated by the character string `uname`. The file is a R data file which contains an `EBImage` image object.

- `seg`: segmentation data, designated by the character string `uname`. The file is a R data file which contains a list of two `EBImage` image objects: `cseg` containing the cell mask and `nseg` the nucleus mask.

- `ftrs`: cell features, designated by the character string `uname`. The file is a tab-separated file which contains the cell features.

- `clabels`: cell labels, designated by the character string `uname`. The file is a tab-separated file which contains the cell labels.

- `viewfull`: calibrated JPEG image, designated by the character string `uname`. The file is a JPEG image.

- `viewunmonted`: spot-untiled calibrated JPEG image, designated by the character string `uname` and the spot number `spot`. The file is a JPEG image.

- `viewseg`: segmented JPEG image, designated by the character string `uname`. The file is a JPEG image.

- `viewthumb`: thumbnail JPEG image, designated by the character string `uname`. The file is a JPEG image.

`readHTS` reads and returns the corresponding file. `format` must be specified if `type` is `file` or `source`.

### Value

`fileHTS` returns a character vector containing the path or URL of the requested file. `readHTS` returns the content of the requested file.

### Author(s)

Gregoire Pau, gregoire.pau@embl.de, 2010

### See Also

`parseImageConf`, `getUnames`

### Examples

    ## initialize imageHTS object using the local submorph screen
    local = tempdir()
    server = system.file('submorph', package='imageHTS')
    x = parseImageConf('conf/imageconf.txt', localPath=local, serverURL=server)

    ## fileHTS and readHTS examples
    fileHTS(x, 'file', filename='conf/imageconf.txt')
    fileHTS(x, 'source', uname='001-01-C05', channel=1)
    readHTS(x, 'file', filename='conf/featurepar.txt', format='dcf')

    ## initialize imageHTS object using the remote kimorph screen
    local = tempdir()
    server = 'http://www.ebi.ac.uk/huber-srv/cellmorph/kimorph/'
    x = parseImageConf('conf/imageconf.txt', localPath=local, serverURL=server)

    ## get cell features for well '002-02-D06'
    f = readHTS(x, 'ftrs', uname='002-02-D06')
    cat('nb cells=', nrow(f), '\n')

[Package imageHTS version 1.36.0 Index]