importGeneSetsFromGMT {singleCellTK} | R Documentation

## Imports gene sets from a GMT file

### Description

Converts a list of gene sets stored in a GMT file into a GeneSetCollection and stores it in the metadata of the SingleCellExperiment object. These gene sets can be used in downstream quality control and analysis functions in singleCellTK.

### Usage

    importGeneSetsFromGMT(
      inSCE,
      file,
      collectionName = "GeneSetCollection",
      by = "rownames",
      sep = "\t"
    )

### Arguments

`inSCE` | Input SingleCellExperiment object.
`file` | Character. Path to GMT file. See getGmt for more information on reading GMT files.
`collectionName` | Character. Name of collection to add gene sets to. If this collection already exists in `inSCE`, then these gene sets will be added to that collection. Any gene sets within the collection with the same name will be overwritten. Default `GeneSetCollection`.
`by` | Character, character vector, or NULL. Describes the location within `inSCE` where the gene identifiers in `geneSetList` should be mapped. If set to `"rownames"` then the features will be searched for among `rownames(inSCE)`. This can also be set to one of the column names of `rowData(inSCE)` in which case the gene identifies will be mapped to that column in the `rowData` of `inSCE`. `by` can be a vector the same length as the number of gene sets in the GMT file and the elements of the vector can point to different locations within `inSCE`. Finally, `by` can be `NULL`. In this case, the location of the gene identifiers in `inSCE` should be saved in the description (2nd column) of the GMT file. See featureIndex for more information. Default `"rownames"`.
`sep` | Character. Delimiter of the GMT file. Default `"\t"`.

### Details

The gene identifiers in gene sets in the GMT file will be mapped to the rownames of `inSCE` using the `by` parameter and stored in a GeneSetCollection object from package GSEABase. This object is stored in `metadata(inSCE)$sctk$genesets`, which can be accessed in downstream analysis functions such as runCellQC.

### Value

A SingleCellExperiment object with gene set from `collectionName` output stored to the metadata slot.

### Author(s)

Joshua D. Campbell

### See Also

importGeneSetsFromList for importing from lists, importGeneSetsFromCollection for importing from GeneSetCollection objects, and importGeneSetsFromMSigDB for importing MSigDB gene sets.

### Examples

    data(scExample)

    # GMT file containing gene symbols for a subset of human mitochondrial genes
    gmt <- system.file("extdata/mito_subset.gmt", package = "singleCellTK")

    # "feature_name" is the second column in the GMT file, so the ids will
    # be mapped using this column in the 'rowData' of 'sce'. This
    # could also be accomplished by setting by = "feature_name" in the
    # function call.
    sce <- importGeneSetsFromGMT(inSCE = sce, file = gmt, by = NULL)

[Package singleCellTK version 2.0.0 Index]