parseImageConf: Instantiate an imageHTS object

Description

Instantiate an imageHTS object from a local or remote screen data repository.

Usage

parseImageConf(filename, localPath='myscreen', serverURL, access='cache')

Arguments

filename

A character string containing the name of the imageHTS configuration file. See Details.

localPath

A character string indicating the path to the project directory that contains (or will contain) the screen data. The directory must be writable and will be created if missing. All intermediate files created by imageHTS will be stored in this directory. Default is myscreen.

serverURL

An optional character string indicating the URL or path to the server from where to download the data, if not available in the local path.

access

A character string indicating how to access the data. Valid values are cache (the default), local and server. See fileHTS for details.

Value

An imageHTS object.

Details

parseImageConf gets access to the configuration file depending on the value of the access argument. If local, the file is loaded from the local path; if server, from the server and if cache parseImageConf tries to first load the file from the local path, and if not present, downloads it from the server. This dual repository feature is useful when screen images are stored in a different location from where they are analysed. See fileHTS for details. The imageHTS configuration file is a DCF file which contains the following fields:

AssayName: a character string containing the name of the assay
SourceFilenamePattern: a character string containing the source image pattern path, relative to the local path. Special fields: {plate}, {replicate}, {row}, {col} and {channel} will be replaced by elements of the corresponding fields PlateNames, ReplicateNames, RowNames, ColNames and ChannelNames.
PlateNames: a comma-separated character vector, containing the plate names, to replaced in the field {plate} of SourceFilenamePattern.
ReplicateNames: same as PlateNames for the field {replicate}.
RowNames: same as PlateNames for the field {row}.
ColNames: same as PlateNames for the field {col}.
ChannelNames: same as PlateNames for the field {channel}.
Montage: an optional comma-separated vector of two integers. If source images contain assembled different spot images of the well, this vector contains the dimension of the montage.

Use the command getImageConf to retrieve the configuration file from an imageHTS object.

Examples

Run this code

local = tempdir()
server = system.file('submorph', package='imageHTS')
x = parseImageConf('conf/imageconf.txt', localPath=local, serverURL=server)
getImageConf(x)

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