ARTP (version 2.0.5)

plot_genes: Gene Plot

Description

Plot the observed SNP p-values for each gene

Usage

plot_genes(obs.outfile, gene.list, op=NULL)

Arguments

obs.outfile

The output file of observed p-values from runPermutations

gene.list

See gene.list

op

List of options. See details.

Value

A data frame containing the SNP ids, parameter estimates, genes, etc.

Details

If the option gene.list$chrm.var is not specified, then it is assumed that all the SNPs are on the same chromosome, and the same color will be used in the plot. If gene.list$chrm.var is specified, then the genes will be grouped by chromosome with the same color for the group.

Options list: Below are the names for the options list op.

• cex.axis See par

• colors Colors to use for each gene in the plot

• maxLabelLen Maximum length of x-axis labels

• chr.text See par

• x.las See par

• x.padj See par

See Also

runPermutations

Examples

# NOT RUN {
 # Get the file of observed p-values
 obs_file <- system.file("sampleData", "obs_pvalues.txt", package="ARTP")

 # Define the gene-SNP list
 gs_file <- system.file("sampleData", "gene_SNP_data.txt", package="ARTP") 
 gene.list <- list(file=gs_file, delimiter="\t", header=1, 
                   snp.var="SNP", gene.var="Gene")
 
 plot_genes(obs_file, gene.list) 
  
# }