setGeneTable: setGeneTable

In snplist: Tools to Create Gene Sets

Description

Takes a data.frame object with columns 'gene','chr','start', and 'end', and creates an SQLite table of the information. Returns a count of the number of genes in the table.

Usage

    setGeneTable(geneInfo,table='gene',db='snplistdb') 

Arguments

geneInfo	A data.frame object of gene location info with columns 'gene','chr','start', and 'end'.
table	Name of the SQLite table to be created. Default is 'gene'.
db	Name of the SQLite database in which to create table. Default is 'snplistdb'.

Value

Count of genes included in table.

Examples

    geneInfo <- cbind(c('BRCA1','BRCA2'),c(17,13),c(41196312,32889611),c(41277500,32973805))
    colnames(geneInfo) <- c('gene','chr','start','end')
    ## Not run: 
    setGeneTable(as.data.frame(geneInfo))
    
## End(Not run)

snplist documentation built on Oct. 9, 2021, 5:06 p.m.