get_qqplot: Create a quantile-quantile plot with ggplot2.
In Alice-MacQueen/snpdiver: Explore SNP Effects on Multiple Phenotypes in Diversity Panels
Description
Usage
Arguments
Value
Description
Assumptions for this quantile quantile plot:
Expected P values are uniformly distributed.
Confidence intervals assume independence between tests.
We expect deviations past the confidence intervals if the tests are
not independent.
For example, in a genome-wide association study, the genotype at any
position is correlated to nearby positions. Tests of nearby genotypes
will result in similar test statistics.
Usage
1
get_qqplot(ps, X = NULL, ind = NULL, ci = 0.95, lambdaGC = FALSE, tol = 1e-08)
Arguments
ps
Numeric vector of p-values.
X
a gwas_effects FBM object
ind
The column number containing the -log10p-values in the FBM object.
ci
Numeric. Size of the confidence interval, 0.95 by default.
lambdaGC
Logical. Add the Genomic Control coefficient as subtitle to
the plot?
tol
Numeric. Tolerance for optional Genomic Control coefficient.
Value
A ggplot2 plot.
Alice-MacQueen/snpdiver documentation built on Dec. 17, 2021, 8:41 a.m.
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Description Usage Arguments Value
Description
Assumptions for this quantile quantile plot: Expected P values are uniformly distributed. Confidence intervals assume independence between tests. We expect deviations past the confidence intervals if the tests are not independent. For example, in a genome-wide association study, the genotype at any position is correlated to nearby positions. Tests of nearby genotypes will result in similar test statistics.
Usage
1 | get_qqplot(ps, X = NULL, ind = NULL, ci = 0.95, lambdaGC = FALSE, tol = 1e-08)
|
Arguments
ps |
Numeric vector of p-values. |
X |
a gwas_effects FBM object |
ind |
The column number containing the -log10p-values in the FBM object. |
ci |
Numeric. Size of the confidence interval, 0.95 by default. |
lambdaGC |
Logical. Add the Genomic Control coefficient as subtitle to the plot? |
tol |
Numeric. Tolerance for optional Genomic Control coefficient. |
Value
A ggplot2 plot.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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