ImmuneSpaceConnection-class {ImmuneSpaceR} | R Documentation |
A connection respresents a study or a set of studies available on ImmuneSpace. It provides function to download and display the data within these studies.
Uses global variables labkey.url.base
, and labkey.url.path
, to
access a study. labkey.url.base
should be
https://www.immunespace.org/
. labkey.url.path
should be
/Studies/studyname
, where 'studyname' is the accession number of the
study.
The ImmunespaceConnection will initialize itself, and look for a
.netrc
file in "~/"
the user's home directory. The
.netrc
file should contain a machine
, login
, and
password
entry to allow access to ImmuneSpace, where machine
is
the host name like "www.immunespace.org".
An instance of an ImmuneSpaceConnection for a study in 'labkey.url.path'
study
A character
. The study accession number. Use an empty
string ("") to create a connection at the project level.
config
A list
. Stores configuration of the connection object
such as URL, path and username.
available_datasets
A data.table
. The table of datasets available
in the connection object.
data_cache
A list
. Stores the data to avoid downloading the same
tables multiple times.
constants
A list
. Used to store information regarding
gene-expression data.
addTreatment(matrixName = NULL)
Add treatment information to the phenoData of an expression matrix available in the connection object.
x: A character. The name of a expression matrix that has been downloaded from the connection.
clear_cache()
Clear the data_cache. Remove downloaded datasets and expression matrices.
EMNames(EM = NULL, colType = "participant_id")
Change the sampleNames of an ExpressionSet fetched by getGEMatrix using the information in the phenodData slot.
x: An ExpressionSet, as returned by getGEMatrix.
colType: A character. The type of column names. Valid options are 'expsample_accession' and 'participant_id'.
getDataset(x, original_view = FALSE, reload = FALSE, colFilter = NULL,
...)
Get a dataset form the connection
original_view: A logical. If set tot TRUE, download the ImmPort view. Else, download the default grid view.
reload: A logical. Clear the cache. If set to TRUE, download the dataset, whether a cached version exist or not.
colFilter: A character. A filter as returned by Rlabkey's makeFilter function.
'...': Extra arguments to be passed to labkey.selectRows.
getGEAnalysis(...)
Downloads data from the gene expression analysis results table.
'...': A list of arguments to be passed to labkey.selectRows.
getGEFiles(files, destdir = ".", quiet = FALSE)
Download gene expression raw data files.
files: A character. Filenames as shown on the gene_expression_files dataset.
destdir: A character. The local path to store the downloaded files.
getGEMatrix(matrixName = NULL, cohort = NULL, outputType = "summary",
annotation = "latest", reload = FALSE)
Downloads a normalized gene expression matrix from ImmuneSpace.
‘x’: A ‘character’. The name of the gene expression matrix to download.
‘cohort’: A ‘character’. The name of a cohort that has an associated gene expression matrix. Note that if ‘cohort’ isn't NULL, then ‘x’ is ignored.
‘outputType’: one of 'raw', 'normalized' or 'summary'. If 'raw' then returns an expression matrix of non-normalized values by probe. 'normalized' returns normalized values by probe. 'summary' returns normalized values averaged by gene symbol.
‘annotation’: one of 'default', 'latest', or 'ImmSig'. Determines which feature annotation set is used. 'default' uses the fas from when the matrix was generated. 'latest' uses a recently updated fas based on the original. 'ImmSig' is specific to studies involved in the ImmuneSignatures project and uses the annotation from when the meta-study's manuscript was created.
‘reload’: A ‘logical’. If set to TRUE, the matrix will be downloaded again, even if a cached cop exist in the ImmuneSpaceConnection object.
getParticipantData(group, dataType, original_view = FALSE, ...)
returns a dataframe with ImmuneSpace data subset by groupId.
group: Use con$listParticipantGroups() to find Participant groupId or groupName.
dataType: Use con$listDatasets('datasets') to see possible dataType inputs.
listDatasets(output = c("datasets", "expression"))
List the datasets available in the study or studies of the connection.
listGEAnalysis()
List available gene expression analysis for the connection.
listParticipantGroups()
returns a dataframe with all saved Participant Groups on ImmuneSpace.
quick_plot(...)
Plots a selected dataset. This is the function used by the DataExplorer module on ImmuneSpace.
dataset: A character. The name of the dataset to plot, as displayed by the listDataset method.
normalize_to_baseline: A logical. If set to TRUE, the values are plotted as log2 fold-change from baseline.
type: A character. The type of plot. Valid choices are 'auto', 'heatmap', 'boxplot', 'lineplot', 'violinplot'. If set to 'auto', the function will select an appropriate plot type for the selected data.
filter: A filter as created by the makeFilter function from Rlabkey.
facet: The facetting for ggplot2 based plots. Valid choices are 'grid' and 'wrap'.
text_size: The size of all text elements in the plot.
legend: A character. Columns of the dataset or demographics to be added as legend on the heatmap. This argument is ignored if the plot type isn't heatmap.
show_virus_strain: A logical. Should all the virus strains be shown or should the values be averaged. Only used when dataset = 'hai'.
interactive: A logical. If set to TRUE, an interactive plot will be created. The default is FALSE.
'...': Extra argument to be passed to ggplot. e.g: shape = 'Age', color = 'Race'.
CreateConnection
ImmuneSpaceR-package
## Not run: sdy269 <- CreateConnection("SDY269") sdy269 ## End(Not run)