retrieveMatrix: Download data from magma that is stored as a matrix
In magmaR: R-Client for 'Magma' of the 'UCSF Mount Etna Data Library'

Description Usage Arguments Value Examples

Download data from magma that is stored as a matrix

retrieveMatrix(
  target,
  projectName,
  modelName,
  recordNames = "all",
  attributeNames,
  filter = "",
  page = NULL,
  pageSize = 10,
  ...
)

`target`	A list, which can be created using `magmaRset`, containing your authorization 'token' (a string), a 'url' of magma to target (a string), and optional 'opts' for specifying additions parameters for curl requests (a named list).
`projectName`	Single string. The name of the project you would like to interact with. For options, see `retrieveProjects`.
`modelName`	Single string. The name of the subset data structure within the project, which are referred to as 'model's in magma, to interact with. For options, see `retrieveModels` or https://timur.ucsf.edu/<projectName>/map.
`recordNames`	Single string or string vector indicating which particular sample/tube/etc. records to target. Options are "all" or any combination of individual record names. To retrieve individual options, see `retrieveIds`.
`attributeNames`	Single string or string vector indicating which features of the data to target. Options are "all" or any combination of individual attribute names. To retrieve individual options, see `retrieveAttributes`.
`filter`	String. Potential filter(s) of the data. Example: "<targetAttributeName>~GYN" to filter to records where <targetAttributeName> contains "GYN". Refer to https://mountetna.github.io/magma.html#retrieve for more details about options and format.
`page`	Integer. For retrieving just a portion of the data, sets which slice to get.
`pageSize`	Integer. For retrieving just a portion of the data, sets slice/page size, which is equivalent to the a number of rows.
`...`	Additional parameters passed along to the internal '.retrieve()', '.query()', or '.update()' functions, for troubleshooting or advanced-user purposes only: `request.only` (Logical) & `json.params.only` (Logical) which 1) stop the function before its main curl request to magma and 2) returns the values that would have been sent to magma in either of two formats. `verbose` (Logical) sets whether to report the status of the curl request after it is performed.

a matrix

if (interactive()) {
    # First, we use magmaRset to create an object which will tell other magmaR
    #  functions our authentication token (as well as some other optional bits).
    # When run in this way, it will ask you to give your token.
    magma <- magmaRset()
    
    retrieveMatrix(
        target = magma,
        projectName = "example",
        modelName = "rna_seq",
        recordNames = "all",
        attributeNames = "gene_counts")
}