writeGenes: Description of features using package 'biomaRt'.

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/functions.R

Description

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

Usage

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  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

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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)

Bioconductor-mirror/MineICA documentation built on May 29, 2017, 8:30 a.m.