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Create OmicSignatureCollection

Vanessa Mengze Li

10/24/2024

CreateOmSC.Rmd
devtools::load_all(".")
#> Error in get(paste0(generic, ".", class), envir = get_method_env()) : 
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library(dplyr)

Create an OmicSignatureCollection Object

This object contains several OmicSignature objects to facilitate further analysis.

An OmicSignatureCollection object contains two parts:
- metadata
- OmicSigList, a list of OmicSignature Objects

1. Metadata for the Collection

The required fields for metadata are:
“collection_name”, “description”.
Additional optional fields can be added.

ColMeta <- list(
  "collection_name" = "Example_Collection",
  "description" = "An example of signature collection",
  "organism" = "Mus Musculus",
  "author" = "me"
)

2. Prepare OmicSignature objects

Create or read OmicSignature objects.
The following signatures are pseudo results for illustration purpose.

OmicObj1 <- readJson(file.path(system.file("extdata", package = "OmicSignature"), "OmS_example_1.json"))
#>   [Success] OmicSignature object Experiment in liver created.
OmicObj2 <- readJson(file.path(system.file("extdata", package = "OmicSignature"), "OmS_example_2.json"))
#>   [Success] OmicSignature object Experiment in brain created.
OmicObj3 <- readJson(file.path(system.file("extdata", package = "OmicSignature"), "OmS_example_3.json"))
#>   [Success] OmicSignature object Experiment in heart created.

3. Create an OmicSignatureCollection object

Use OmicSignatureCollection$new() and provide metadata and a list of OmicSignature objects:

OmicCol <- OmicSignatureCollection$new(
  OmicSigList = list(OmicObj1, OmicObj2, OmicObj3),
  metadata = ColMeta,
  print_message = FALSE
)

During the creation of OmicSignatureCollection, all input OmicSignature objects will be re-created to make sure they pass all the check functions.