download {FlowRepositoryR} | R Documentation |
This method can download whole datasets (all FCS files and attachments of
a flowRepData
object) or individual files based on
file proxies (fileProxy
objects).
download(object, ...)
object |
Object of class |
... |
Additional options, see the details section. |
The full dataset or the file represented by the file proxy will be
downloaded to the local file system. If you are downloading the
whole dataset (passing a flowRepData
object),
then you can specify the following additional options:
dirpath=NULL
The path to the directory where to download the files. By default, the files will be downloaded to a folder named based on the dataset identifier (FR-FCM-xxxx) that will be created in your working directory.
use.credentials=TRUE
Whether to use stored credentials
to login before downloading the dataset.
Credentials will only be used if use.credentials=TRUE
and they are set (see setFlowRepositoryCredentials
).
If your credentials are set, but you are downloading a public
dataset that does not need credentials, then you can use
use.credentials=FALSE
to avoid logging in.
show.progress=TRUE
Whether to show progress as individual files are being downloaded.
only.files=NULL
If not NULL then download only files
with names matching a regular expression specified as a single
string of characters in this argument. For example, the regular
expression "pA.*fcs" will download only files whose name starts with
"pA" and ends with "fcs"; the ".*" part of the regular expression
means any character (.) repeated 0 or more times (*). This
particular example can be used to download FCS files from IMPC
panel A as their names are created as
pA_specimenId_incrementvalue.fcs
.
Files will be skipped if the regular expression does not match.
If you are downloading a single file by (passing a
fileProxy
object), then you can specify the
following additional options:
dirpath=NULL
The path to the directory where to download
the file. By default, the file will be downloaded to your working
directory. A filepath
argument as specified below takes
precedence over the dirpath
argument.
filepath=NULL
The path where to download the file.
If provided, this argument takes precedence over dirpath
.
curlHandle=getCurlHandle(cookiefile="")
Used to pass cookies to keep track of sessions. This is intended for internal use, not to be used by regular users.
show.progress=TRUE
Whether to show progress as the file is being downloaded.
only.files=NULL
If not NULL then download the file only
if its name is matching a regular expression specified as a single
string of characters in this argument. For example, the regular
expression "pA.*fcs" will download only files whose name starts with
"pA" and ends with "fcs"; the ".*" part of the regular expression
means any character (.) repeated 0 or more times (*). This
particular example can be used to download FCS files from IMPC
panel A as their names are created as
pA_specimenId_incrementvalue.fcs
.
The file will be skipped if the regular expression does not match.
A fileProxy
object if object
is a
fileProxy
object or
a flowRepData
object if object
is a
flowRepData
object.
This is an updated file proxy or a dataset that includes local path
to the downloaded files.
Josef Spidlen
## We will get a small dataset myDataset <- flowRep.get("FR-FCM-ZZJ7") summary(myDataset) ## And download a single attachment file ## mainly just to demonstrate that one can do one file at a time. att1 <- download(attachments(myDataset)[[1]]) localpath(att1) ## We can also find out about individual FCS file proxies summary(fcs.files(myDataset)[[1]]) ## A single FCS file proxy can be downloaded fcs1 <- download(fcs.files(myDataset)[[1]]) summary(fcs1) ## The file is downloaded to your home directory localpath(fcs1) ## The code above is just to demonstrate that it is ## possible to get individial files. However, typically, ## we will want to download the whole dataset. myDataset <- download(myDataset) summary(myDataset) ## This downloaded all the files to your home directory ## This is where you find your data unlist(lapply(fcs.files(myDataset), function(x) paste(localpath(x)))) ## And this is where you find the attachments of that dataset unlist(lapply(attachments(myDataset), function(x) paste(localpath(x))))