singlePlotRACER: Single Regional Association Plot Function
In oliviasabik/RACER: Regional Association Comparer

Description Usage Arguments Examples

View source: R/singlePlotRACER.R

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.

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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)

`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.

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)