'fcsProxy': a class representing a proxy to an FCS file in FlowRepository

Description

This class represents basic metadata (i.e., information about) a single FCS file in FlowRepository.

Details

Objects of class fcsProxy are used to hold information about a FlowRepository FCS file. This information includes the file name, URL, size in bytes, MD5 sum, FCS version and a path to the file on the local file system. A NULL value in the localpath slot indicates that the FCS file has not been downloaded, you can use the download method to download the file.

Creating Objects

Objects of the fcsProxy class are created automatically when you create a flowRepData object from FlowRepository by calling the flowRep.get. A list of fcsProxy objects will be placed in the fcs.files slot of the flowRepData object.

Unless you know what you are doing, creating objects using new or the constructor (as described below) is discouraged.

Objects can be created using
new("fcsProxy",
name = ...., Object of class character
url = ...., Object of class character
size = ...., Object of class numeric
md5sum = ...., Object of class character or NULL
fcs.version = ...., Object of class character or NULL
localpath = ...., Object of class character or NULL
)

or the constructor fcsProxy, with mandatory arguments name and url and optional arguments size, md5sum, fcs.version and localpath.

fcsProxy(name, url, size=0, md5sum=NULL,
fcs.version=NULL, localpath=NULL)

Slots

name:

Object of class character containing the name of the FlowRepository FCS file.

url:

Object of class character containing the url of the FlowRepository FCS file.

size:

Object of class numeric containing the size of the FlowRepository FCS file in bytes.

md5sum:

Object of class character or NULL containing the MD5 sum of the FlowRepository FCS file.

fcs.version:

Object of class character or NULL containing the FCS version identifier of the FlowRepository FCS file. This version identifier corresponds to the first 6 bytes of the FCS file and typically contains one of the following strings: FCS1.0, FCS2.0, FCS3.0, or FCS3.1.

localpath:

Object of class character or NULL containing the path the FlowRepository FCS file as saved on the local file system. This slot is used to determine whether the file has been downloaded to the local file system. A value of NULL indicates that the FCS file has not been downloaded. The download method can be used to download the file.

Extends

Class fileProxy, directly.

Methods

There are separate documentation pages for some of the methods listed here which may be consulted for more details.

summary

Print a basic summary about an fcsProxy. See summary for details. Usage: summary(fcsProxy)

download

Download the referenced FCS file to the local file system, fill out the localpath slot and return an updated copy of the fcsProxy object. See download for details. Usage: download(fcsProxy, dirpath=NULL, filepath=NULL,
curlHandle=getCurlHandle(cookiefile=""),
show.progress=TRUE, ...)

is.downloaded

Return TRUE if the localpath slot is not NULL, which indicates that the file has been downloaded to the local file system. Return FALSE if the localpath is NULL. See is.downloaded for details. Usage: is.downloaded(fcsProxy)

Author(s)

Josef Spidlen

References

Josef Spidlen, Wayne Moore, David Parks, Michael Goldberg, Chris Bray, Pierre Bierre, Peter Gorombey, Bill Hyun, Mark Hubbard, Simon Lange, Ray Lefebvre, Robert Leif, David Novo, Leo Ostruszka, Adam Treister, James Wood, Robert F. Murphy, Mario Roederer, Damir Sudar, Robert Zigon, and Ryan R. Brinkman.
Data File Standard for Flow Cytometry, Version FCS 3.1
Cytometry A. 2010 Jan; 77(1): 97100. doi: 10.1002/cyto.a.20825
http://tinyurl.com/fcs3-1-pdf

See Also

fileProxy, attachmentProxy, flowRepData, download

Examples

1
2
3
    myDataset <- flowRep.get("FR-FCM-ZZZG")
    summary(fcs.files(myDataset)[[1]])
    str(fcs.files(myDataset)[[1]])

Want to suggest features or report bugs for rdrr.io? Use the GitHub issue tracker.