get_qqplot: Create a quantile-quantile plot with ggplot2.
In Alice-MacQueen/CDBNgenomics: Genomics Using the Cooperative Dry Bean Nursery Dataset
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, ci = 0.95, lambdaGC = FALSE, tol = 1e-08)
Arguments
ps
Numeric vector of p-values.
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/CDBNgenomics documentation built on Aug. 18, 2020, 4:39 p.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, ci = 0.95, lambdaGC = FALSE, tol = 1e-08)
|
Arguments
ps |
Numeric vector of p-values. |
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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