GeneAnswers (version 2.14.0)

getListGIF: getListGIF

Description

Function to grab the overrepresented concepts from a list of genes throught ListGIF web server.

Usage

getListGIF(glist, output=NULL, background=c("white", "black"), type=c("genelevel", "riflevel", "goterm"))

Arguments

glist

a character vector or a list or an one-column data frame giving gene symbols for query

output

a character string specifying the name of the word cloud figure. Default is NULL, in this case the file name is generated by ListGIF web server

background

a character string specifying the background of the word cloud png file to be either "white"" or "black". Default is "white""

type

a character string specifying the type of analysis implemented by ListGIF web server: "genelevel", "riflevel" or "goterm". Default is "genelevel"

Value

A png file is generated at current working directory if user-specified directory is not provided in the output argument.

Details

glist is a character vector of gene symbols in query. If glist is a list or a one-column data frame, it will be converted to a vector. output is the file name of the word cloud graph. If not specified, the original file name generated by ListGIF server is provided. background of the word cloud graph can be either white or black. Default is white. type specifies the word cloud to be eigher geneGIF, geneRIF or GO terms. geneRIF analysis requires considerable amount of time.

References

Wen, J., Wang X., Kibbe, W., Lin S., Lu, H., 'Visual Annotation of the Gene Database', Conf Proc IEEE Eng Med Biol Soc. 2009;2009:4175-7

Examples

glist <- c("MRPS35","NBL1","PSMD14","PGK1","SMC4","SLC16A1","CAV1")
## Not run: getListGIF(glist=glist)
## Not run: getListGIF(glist=glist, output="tmp2.png", background="black", type="riflevel")