formatRACER.Rd
This group of functions 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. This function carries out the formatting necessary to generate a plot
formatRACER(assoc_data, chr_col, pos_col, p_col = NULL, log10p_col = NULL, ld_col = NULL, rs_col = NULL)
assoc_data | required. A dataframe that has columns containing the chromosome, physical position, and p-values or -log10(p-values) of the association, and can optionally have columns containing R2 information for LD in the region, or rsID numbers for the associated SNPs |
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chr_col | required. numeric. index of column in assoc_data containing chromosome information |
pos_col | required. numeric. index of column in assoc_data containing genomic position information |
p_col | required, if no log10p_col column specified. numeric. index of column in assoc_data containing p-values |
log10p_col | required, if no p_col specified. numeric. index of column in assoc_data containing -log10(p-value)s |
ld_col | optional. numeric. Required if you want to use the LD data in your data set in your plot, index of column in assoc_data containing LD information, e.g. R2 or D' values |
rs_col | optional. numeric. Required if you want to use the use ldRACER to pull LD information from the 1000 genomes phase III project, or if you want to make a scatter comparison plot |
# NOT RUN { data(mark3_bmd_gwas) head(formatRACER(assoc_data = mark3_bmd_gwas, chr_col = 3, pos_col = 4, p_col = 11, rs_col = 2)) # }