mirrorPlotRACER: Mirror Plot - Regional Association ComparER Plot

In oliviasabik/mirrorplot: Regional Association Comparer

Mirror Plot – Regional Association ComparER Plot

Description

This function allows you to creat a plot of -log10(P-values) for two sets of association data. Mirror plots illustrate the two associations on a common x-axis, with the first association inverted, mirroring the two associations against one another.

Usage

mirrorPlotRACER(assoc_data1, assoc_data2, chr, build = "hg19",
  set = "protein_coding", name1 = "Association Dataset #1",
  name2 = "Association Dataset #2", plotby, gene_plot = NULL,
  snp_plot = NULL, start_plot = NULL, end_plot = NULL,
  label_lead = FALSE)

Arguments

assoc_data1	required. A dataframe that has columns named POS representing the position of the SNP on the chromosome, LOG10P which contains the -log10(P-values), CHR, which contains the chromosome number, RS_ID, which contains LD information. If your data set has been processed using the formatRACER function and the ldRACER function, these columns will be appropriately named in your data.
assoc_data2	required. identifcal in format to assoc_data1
chr	required. chromosome you wish to plot
build	optional. indicates the genome build to use to plot the genes below the association plot. default = "hg19", but can be changed to "hg38"
set	optional. default = "protein_coding", however can be set to "all" to plot all RNAs in the genome
name1	optional. name of association set 1
name2	optional. name of association set 2
plotby	required. "coord", "gene", or "snp". Which parameter to use to determine the reigon to be plotted.
gene_plot	optional. If "gene" selected for plotby, then plot will be +/- 50kb of gene, should be a human gene symbol
snp_plot	optional. If "snp" selected for plotby, then plot will be +/- 50kb of snp
start_plot	optional. If "coord" selected for plotby, then this will be lower bound of x-axis
end_plot	optional. 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. Labels both plots.

Examples

data(mark3_bmd_gwas)
data(mark3_eqtl)

mark3_bmd_gwas_f = RACER::formatRACER(assoc_data = mark3_bmd_gwas, chr_col = 3,
pos_col = 4, p_col = 11)
mark3_eqtl_f = RACER::formatRACER(assoc_data = mark3_eqtl, chr_col = 10,
pos_col = 11, p_col = 7)

mark3_bmd_gwas_f_ld = RACER::ldRACER(assoc_data = mark3_bmd_gwas_f,
rs_col = 2, pops ="EUR", lead_snp = "rs11623869")
mark3_eqtl_f_ld = RACER::ldRACER(assoc_data = mark3_eqtl_f,
rs_col = 15, pops = "EUR", lead_snp = "rs11623869")
mirrorPlotRACER(assoc_data1 = mark3_bmd_gwas_f_ld, assoc_data2 = mark3_eqtl_f_ld,
chr = 14, plotby = "gene", gene_plot = "MARK3")

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