Description Usage Arguments Details
A scatter plot of negative log base 10 p-value against genomic position
1 2 3 4 5 6 7 8 9 10 11 12 13 14 |
data |
A genetic association results dataframe. |
trait_label |
A character vector to be used as label. Default = "phenotype". |
trim |
Observations with p-values larger than the trim value are dropped. Default = 0.001. |
chromosome |
An integer vector of chromosome codes. |
snp |
SNP id. |
bp |
Base-pair coordinate. |
a1 |
Allele 1 (usually minor). See details. |
effect |
Regression coefficient or odds ratio. |
p |
Association p-value. |
chr_color |
A character vector of 2 colours to be used on alternate chromosomes. |
strip_color |
Color of the vertical strip describing the panel. |
... |
Additional arguments passed to |
SNP id (snp
), Allele 1 (a1
), and regression
coefficient or odds ratio (effect
) columns are only used for
labelling points. a1
is described as it is in
PLINK
documentation, but as this column is only used for labelling it can
refer to any allele. PLINK output names are used as the default
values for all columns.
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