writeGenes {MineICA} | R Documentation

## Description of features using package `biomaRt`.

### Description

This function annotates IDs (typically gene IDs) provided by the user and returns an html file with their description.

### Usage

      writeGenes(data, filename = NULL,
        mart = useMart(biomart = "ensembl", dataset = "hsapiens_gene_ensembl"),
        typeId = "hgnc_symbol", typeRetrieved = NULL,
        sortBy = NULL, sortAbs = TRUE, colAnnot = NULL,
        decreasing = TRUE, highlight = NULL, caption = "")

### Arguments

`data` | Either a data.frame whose rownames or one of its columns contain the IDs to be annotated, or a vector of IDs.
`filename` | The name of the HTML file where gene annotations are written.
`mart` | Output of function `useMart` from package `biomaRt`.
`typeId` | The type of IDs available in `data`, in the biomaRt way (type `listFilters(mart)` to choose one).
`typeRetrieved` | The descriptors uses to annotate the features of `data` (type `listAttributes(mart)` to choose one or several).
`sortBy` | Name of a column of `data` used to order the output.
`sortAbs` | If TRUE absolute value of column `sortBy` is used to order the output.
`colAnnot` | The column containing the IDs to be annotated, if NULL or missing and argument `data` is a data.frame, then rownames of `data` must contain the IDs.
`decreasing` | If TRUE, the output is sorted by decreasing values of the `sortBy` column
`highlight` | IDs to be displayed in colour red in the returned table
`caption` | A title for the HTML table

### Details

`"hgnc_symbol", "ensembl_gene_id", "description", "chromosome_name", "start_position", "end_position", "band"`, and `"strand"`, are automatically added to the list of fields available in argument `typeRetrieved` queried on biomaRt. The web-links to www.genecards.org and www.proteinatlas.org are automatically added in the columns of the output respectively corresponding to `hgnc_symbol` and `ensembl_gene_id`.

### Value

This function returns a data.frame which contains annotations of the input data.

### Author(s)

Anne Biton

### See Also

`getBM`, `listFilters`, `listAttributes`, `useMart`

### Examples

    if (interactive()) {
    ## define the database to be used
    mart <- useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl")

    ### Describe:
    ## a set of hgnc symbols with default descriptions (typeRetrieved=NULL)
    genes <- c("TOP2A","E2F3","E2F1","CDK1","CDC20","MKI67")
    writeGenes(data=genes, filename="foo", mart=mart, typeId = "hgnc_symbol")

    ## a data.frame indexed by hngc symbols, sort output according to column "values", add a title to the HTML output
    datagenes <- data.frame(values=rnorm(6),row.names = genes)
    writeGenes(data=datagenes, filename="foo", sortBy = "values", caption = "Description of some proliferation genes.")

    ## a set of Entrez Gene IDs with default descriptions
    genes <- c("7153","1871","1869","983","991","4288")
    writeGenes(data=genes, filename="foo", mart=mart, typeId = "entrezgene")
    }
    ## Not run:
    ## add the GO category the genes belong to
    ## search in listAttributes(mart)[,1] which filter correspond to the Gene Ontology -> "go_id"
    writeGenes(data=genes, filename="foo", mart=mart, typeId = "entrezgene", typeRetrieved = "go_id")

    ## End(Not run)

[Package MineICA version 1.26.0 Index]