read_gmt {pathwayPCA} | R Documentation

## Read a `.gmt` file in as a `pathwayCollection` object

### Description

Read a set list file in Gene Matrix Transposed (`.gmt`) format, with special performance consideration for large files. Present this object as a `pathwayCollection` object.

### Usage

    read_gmt(
      file,
      setType = c("pathways", "genes", "regions"),
      description = FALSE,
      nChars = 1e+07,
      delim = "\t"
    )

### Arguments

`file` | A path to a file or a connection. This file must be a `.gmt` file, otherwise input will likely be nonsense. See the "Details" section for more information.
`setType` | What is the type of the set: pathway set of gene, gene sites in RNA or DNA, or regions of CpGs. Defaults to `''pathway''`.
`description` | Should the "description" field (the second field in the `.gmt` file on each line) be included in the output? Defaults to `FALSE`.
`nChars` | The number of characters to read from a connection. The largest `.gmt` file we have encountered is the full C5 pathway collection from MSigDB (5917 pathways), which has roughly 5 million characters in UTF-8 encoding. Therefore, we default this argument to be twice the size of the largest pathway collection we have seen so far, 10,000,000.
`delim` | The `.gmt` delimiter. As proper `.gmt` files are tab delimited, this defaults to `"\t"`.

### Details

This function uses `R`'s `readChar` function to improve character input performance over `readLines` (and far improve input performance over `scan`).

See the Broad Institute's "Data Formats" page for a description of the Gene Matrix Transposed file format: https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats#GMT:_Gene_Matrix_Transposed_file_format_.28.2A.gmt.29

### Value

A `pathwayCollection` list of sets. This list has three elements:

- 'setType' : A named list of character vectors. Each vector contains the names of the individual genes, sites, or CpGs within that set as a vector of character strings. The name of this list entry is equal to the value specified in `setType`.

- `TERMS` : A character vector the same length as the 'setType' list with the proper names of the sets.

- `description` : (OPTIONAL) A character vector the same length as the 'setType' list with a note on that set (for the `.gmt` file included with this package, this field contains hyperlinks to the MSigDB description card for that pathway). This field is included when `description = TRUE`.

### See Also

`print.pathwayCollection`; `write_gmt`

### Examples

      # If you have installed the package:
      data_path <- system.file(
        "extdata", "c2.cp.v6.0.symbols.gmt",
        package = "pathwayPCA", mustWork = TRUE
      )
      geneset_ls <- read_gmt(data_path, description = TRUE)

      # # If you are using the development version from GitHub:
      # geneset_ls <- read_gmt(
      #   "inst/extdata/c2.cp.v6.0.symbols.gmt",
      #   description = TRUE
      # )

[Package pathwayPCA version 1.8.0 Index]