singlePlotRACER: Single Regional Association Plot Function

In oliviasabik/mirrorplot: Regional Association Comparer

Single Regional Association Plot Function

Description

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. Be sure your input association data has been formatted using formatRACER. If you want to include linkage disequilibirum data, you can use the ldRACER function to use the 1000 genomes project to calculate LD for your data.

Usage

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

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", depending on the build of your input data
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
label_lead	optional. default = FALSE, set = TRUE if you wish to add a label to your graph of the SNP used to calculate LD. If the SNP used to calculate LD is not in your data set, the SNP with the greatest -LOG10(P) will be labeled.

Examples

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)

oliviasabik/mirrorplot documentation built on Dec. 20, 2024, 11:11 p.m.