Single Regional Association Plot Function

This function allows you to creat a plot of -log10(P-values) of an association study by their genomic position, for example, the results of a GWAS or eQTL study. Sources 1000K genomes phase III data for linkage disequilibrium calculations.

singlePlotRACER(assoc_data, chr, build = "hg19",
  set = "protein_coding", plotby, gene_plot = NULL, snp_plot = NULL,
  start_plot = NULL, end_plot = NULL)

Arguments

assoc_data	required. A dataframe that has been produced by formatRACER and has columns named CHR, POS
chr	required. numeric. chromosome to plot
build	optional. default = "hg19", can also optionally be set to "hg38"
set	optional. default = "protein_coding", however can be set to "all" to plot all RNAs in the genome
plotby	required. "coord", "gene", or "snp". Which parameter to use to determine the reigon to be plotted.
gene_plot	optional. Required if "gene" selected for plotby, then plot will be +/- 50kb of gene
snp_plot	optional. Required if "snp" selected for plotby, then plot will be +/- 50kb of snp
start_plot	optional. Required if "coord" selected for plotby, then this will be lower bound of x axis
end_plot	optional. Required if "coord" selected for plotby, then this will be upper bound of x axis

Examples

# NOT RUN {
data(mark3_bmd_gwas)
mark3_bmd_gwas_f = formatRACER(assoc_data = mark3_bmd_gwas, chr_col = 3,
pos_col = 4, p_col = 11)
mark3_bmd_gwas_f_ld = ldRACER(assoc_data = mark3_bmd_gwas_f,
rs_col = 2, pops = c("EUR"), lead_snp = "rs11623869")
singlePlotRACER(assoc_data = mark3_bmd_gwas_f_ld, chr = 14,
build = "hg19", plotby = "coord", start_plot = 103500000, end_plot = 104500000)
# }