ImmuneSpaceConnection {ImmuneSpaceR} | R Documentation

## The ImmuneSpaceConnection class

### Description

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.

### Usage

    ISCon

### Format

An object of class `R6ClassGenerator` of length 24.

### Details

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".

It can also use 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.

### Value

An instance of an ImmuneSpaceConnection for a study in `labkey.url.path`.

### Constructor

`CreateConnection`

### Fields

`study`

  A `character`. The study accession number. Use an empty string ("") to create a connection at the project level.

`availableDatasets`

  A `data.table`. The table of datasets available in the connection object.

`cache`

  A `list`. Stores the data to avoid downloading the same tables multiple times.

`config`

  A `list`. Stores configuration of the connection object such as URL, path and username.

### Methods

`initialize(..., config = NULL)`

  Initialize `ImmuneSpaceConnection` class. See `CreateConnection`.

`print()`

  Print `ImmuneSpaceConnection` class.

`listDatasets(output = c("datasets", "expression"))`

  Lists the datasets available in the study or studies of the connection.

`listGEMatrices(verbose = FALSE, reload = FALSE)`

  Lists available gene expression matrices for the connection.

  `verbose`: A logical. If TRUE, whether to print the extra details for troubleshooting.

  `reload`: A logical. If TRUE, retrieve the table of available gene expression matrices whether a cached version exist or not.

`listGEAnalysis()`

  Lists available gene expression analysis for the connection.

`listParticipantGroups()`

  Lists available participant groups on the ImmuneSpace portal.

`getDataset(x, original_view = FALSE, reload = FALSE, colFilter = NULL, ...)`

  Get a dataset form the connection.

  `x`: A character. The name of the dataset to download.

  `original_view`: A logical. If TRUE, download the original ImmPort view; else, download the default grid view.

  `reload`: A logical. If 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`.

`getGEMatrix(matrixName = NULL, cohort = NULL, outputType = "summary", annotation = "latest", reload = FALSE, verbose = FALSE)`

  Downloads a probe-level or gene-symbol summarized expression matrix from ImmuneSpace. Use experimentData() on the resulting expressionSet object to see version info for annotation.

  `matrixName`: 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 this argument is not NULL, then `matrixName` 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.

  `verbose`: A logical. If set to TRUE, notes on how the expressionSet object was created will be printed, including normalization, summarization, feature_annotation_set, and alias2symbol mapping version of org.Hs.eg.db.

`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)`

  Downloads 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.

`getGEInputs()`

  Downloads data from the gene expression input samples table.

`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.

`addTreatment(matrixName = NULL)`

  Adds treatment information to the phenoData of an expression matrix available in the connection object.

  `matrixName`: A character. The name of a expression matrix that has been downloaded from the connection.

`mapSampleNames(EM = NULL, colType = "participant_id")`

  Changes the sampleNames of an ExpressionSet fetched by `getGEMatrix` using the information in the phenodData slot.

  `EM`: An ExpressionSet, as returned by `getGEMatrix`.

  `colType`: A character. The type of column names. Valid options are 'expsample_accession' and 'participant_id'.

`plot(...)`

  Visualizes a selected dataset. This method is used by the DataExplorer module on the ImmuneSpace portal.

  `dataset`: A character. The name of the dataset to plot, as displayed by the listDataset method.

  `normalize_to_baseline`: A logical. If 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 TRUE, an interactive plot will be created. The default is FALSE.

  `...`: Extra argument to be passed to ggplot. e.g: shape = 'Age', color = 'Race'.

`clearCache()`

  Clears the cache. Removes downloaded datasets and expression matrices.

### See Also

`CreateConnection` `ImmuneSpaceR-package`

### Examples

    ## Not run:
    # Create a connection (Initiate a ImmuneSpaceConnection object)
    sdy269 <- CreateConnection("SDY269")

    # Print the connection object
    sdy269

    # Retrieve the HAI dataset
    HAI <- sdy269$getDataset("hai")

    # Fetch a summarized gene expresssion matrix with latest annotation
    LAIV <- sdy269$getGEMatrix("LAIV_2008")

    # Visualize the ELISA dataset
    sdy269$plot("elisa")

    ## End(Not run)

[Package ImmuneSpaceR version 1.8.2 Index]