CreateOmics {pathwayPCA} | R Documentation

## Generation Wrapper function for `-Omics*`-class objects

### Description

This function calls the `CreateOmicsPath`, `CreateOmicsSurv`, `CreateOmicsReg`, and `CreateOmicsCateg` functions to create valid objects of the classes `OmicsPathway`, `OmicsSurv`, `OmicsReg`, or `OmicsCateg`, respectively.

### Usage

    CreateOmics(
      assayData_df,
      pathwayCollection_ls,
      response = NULL,
      respType = c("none", "survival", "regression", "categorical"),
      centerScale = c(TRUE, TRUE),
      minPathSize = 3,
      ...
    )

### Arguments

`assayData_df` | An N \times p data frame with named columns.
`pathwayCollection_ls` | A `pathwayCollection` list of known gene pathways with two or three elements: `pathways` : A named list of character vectors. Each vector contains the names of the individual genes within that pathway as a vector of character strings. The names contained in these vectors must have non-empty overlap with the column names of the `assayData_df` data frame. The names of the pathways (the list elements themselves) should be the a shorthand representation of the full pathway name. `TERMS`: A character vector the same length as the `pathways` list with the proper names of the pathways. `description` : An optional character vector the same length as the `pathways` list with additional information about the pathways. If your gene pathways list is stored in a `.gmt` file, use the `read_gmt` function to import your pathways list as a `pathwayCollection` list object.
`response` | An optional response object. See "Details" for more information. Defaults to `NULL`.
`respType` | What type of response has been supplied. Options are `"none"`, `"survival"`, `"regression"`, and `"categorical"`. Defaults to `"none"` to match the default `response = NULL` value.
`centerScale` | Should the values in `assayData_df` be centered and scaled? Defaults to `TRUE` for centering and scaling, respectively. See `scale` for more information.
`minPathSize` | What is the smallest number of genes allowed in each pathway? Defaults to 3.
`...` | Dots for additional arguments passed to the internal `CheckAssay` function.

### Details

This function is a wrapper around the four `CreateOmics*` functions. The values supplied to the `response` function argument can be in a list, data frame, matrix, vector, `Surv` object, or any class which extends these. Because this function makes "best guess" type conversions based on the `respType` argument, this argument is mandatory if `response` is non-`NULL`. Further, it is the responsibility of the user to ensure that the coerced response contained in the resulting `Omics` object accurately reflects the supplied response.

For `respType = "survival"`, `response` is assumed to be ordered by event time, then event indicator. For example, if the response is a data frame or matrix, this function assumes that the first column is the time and the second column the death indicator. If the response is a list, then this function assumes that the first entry in the list is the event time and the second entry the death indicator. The death indicator must be a logical or binary (0-1) vector, where 1 or `TRUE` represents a death and 0 or `FALSE` represents right-censoring.

Some of the pathways in the supplied pathways list will be removed, or "trimmed", during object creation. For the pathway-testing methods, these trimmed pathways will have p-values given as `NA`. For an explanation of pathway trimming, see the documentation for the `IntersectOmicsPwyCollct` function.

### Value

A valid object of class `OmicsPathway`, `OmicsSurv`, `OmicsReg`, or `OmicsCateg`.

### See Also

`OmicsPathway`, `CreateOmicsPath`, `OmicsSurv`, `CreateOmicsSurv`, `OmicsCateg`, `CreateOmicsCateg` `OmicsReg`, `CreateOmicsReg`, `CheckAssay`, `CheckPwyColl`, and `IntersectOmicsPwyCollct`

### Examples

      ###  Load the Example Data  ###
      data("colonSurv_df")
      data("colon_pathwayCollection")

      ###  Create an OmicsPathway Object  ###
      colon_OmicsPath <- CreateOmics(
        assayData_df = colonSurv_df[, -(2:3)],
        pathwayCollection_ls = colon_pathwayCollection
      )

      ###  Create an OmicsSurv Object  ###
      colon_OmicsSurv <- CreateOmics(
        assayData_df = colonSurv_df[, -(2:3)],
        pathwayCollection_ls = colon_pathwayCollection,
        response = colonSurv_df[, 1:3],
        respType = "surv"
      )

      ###  Create an OmicsReg Object  ###
      colon_OmicsReg <- CreateOmics(
        assayData_df = colonSurv_df[, -(2:3)],
        pathwayCollection_ls = colon_pathwayCollection,
        response = colonSurv_df[, 1:2],
        respType = "reg"
      )

      ###  Create an OmicsCateg Object  ###
      colon_OmicsCateg <- CreateOmics(
        assayData_df = colonSurv_df[, -(2:3)],
        pathwayCollection_ls = colon_pathwayCollection,
        response = colonSurv_df[, c(1,3)],
        respType = "cat"
      )

[Package pathwayPCA version 1.10.0 Index]