Description Usage Arguments Value
Plots the p-values that test the hypothesis of pleiotropic effects on n_traits. This function also returns a dataframe with information of the significant SNPs.
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pleio_res |
object returned by pleio_test(). |
alpha |
numeric threshold for significance level (Bonferroni correction by default). |
n_traits |
integer indicating the level of pleiotropy to test (a.k.a. number of traits). |
bp_positions |
dataframe with colnames 'chr' and 'pos' indicating the chromosome and position for each SNP. Rownames must contain SNP names matching results of pleio_test. |
set_colors |
string with 3 colors to use in the plot (by default: c('goldenrod4', 'brown4', 'royalblue2')). |
set_text |
dataframe or matrix with strings to add as text to identify SNPs or genes. Rownames must be SNP names matching results of pleio_test. The first column of the dataframe must have strings to plot as text. |
set_plot |
logical indicating whether to return the manhattan plot (TRUE by default). |
chr_spacing |
integer indicating the spacing (in base pair positions) between chromosomes. 1e5 by default. |
... |
additional graphic parameters for the plot. |
Manhattan plot and dataframe with information related to significant SNPs.
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