scatterPlotRACER.RdThis function allows you to create a scatter plot of -log10(P-values).
scatterPlotRACER(assoc_data1, assoc_data2, chr, name1 = "Association Dataset #1", name2 = "Association Dataset #2", region_start, region_end, ld_df = NULL, label = FALSE)
| 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 rsIDs for the SNPs in the data frame. If you have processed your data using formatRACER() these columns will be properly labeled |
|---|---|
| assoc_data2 | required. identifcal in format to assoc_data1 |
| chr | required. chromosome you wish to plot |
| name1 | optional. name of association set 1 |
| name2 | optional. name of association set 2 |
| region_start | start coordinates on chr to be compared |
| region_end | end coordinates on the chr to be compared |
| ld_df | data frame containing the LD data to use to color the plot |
| label | optional. If TRUE, will add a label to a the maximum combined LOG10P of the plot |
# NOT RUN { data("mark3_eqtl") data("mark3_bmd_gwas") df1_f = formatRACER(assoc_data = mark3_bmd_gwas, chr_col = 3, pos_col = 4, p_col = 11,rs_col = 2) df2_f = formatRACER(assoc_data = mark3_eqtl, chr_col = 10, pos_col = 11, p_col = 7,rs_col = 15) df1_f_ld = ldRACER(assoc_data = df1_f, rs_col = 2, pops = "EUR", lead_snp = "rs11623869") df2_f_ld = ldRACER(assoc_data = df2_f, rs_col = 15, pops = "EUR", lead_snp = "rs11623869") scatterPlotRACER(assoc_data1 = df1_f_ld, assoc_data2 = df2_f_ld, chr = 14, name1 = "Mark3_GWAS", name2 = "Mark3_eQTL", region_start = 103750000, region_end = 104250000, ld_df = 1) # }