sHWE: Hardy-Weinberg Equilibrium in structure populations
In lfa: Logistic Factor Analysis for Categorical Data
Description
Usage
Arguments
Value
Examples
Description
Compute structural Hardy-Weinberg Equilibrium (sHWE) p-values
on a SNP-by-SNP basis. These p-values can be aggregated to
determine genome-wide goodness-of-fit for a particular value
of d. See https://doi.org/10.1101/240804 for more
details.
Usage
1
sHWE(X, LF, B)
Arguments
X
a matrix of SNP genotypes, i.e. an integer matrix of 0's,
1's, and 2's. Sparse matrices of class Matrix are not supported
(yet).
LF
matrix of logistic factors
B
number of null datasets to generate - B=1 is usualy
sufficient. If computational time/power allows, a few extra
B could be helpful
Value
a vector of p-values for each SNP.
Examples
1
2
3
4
5
6
LF <- lfa(hgdp_subset, 4)
gof_4 <- sHWE(hgdp_subset, LF, 3)
LF <- lfa(hgdp_subset, 10)
gof_10 <- sHWE(hgdp_subset, LF, 3)
hist(gof_4)
hist(gof_10)
lfa documentation built on Nov. 8, 2020, 7:30 p.m.
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Description Usage Arguments Value Examples
Description
Compute structural Hardy-Weinberg Equilibrium (sHWE) p-values on a SNP-by-SNP basis. These p-values can be aggregated to determine genome-wide goodness-of-fit for a particular value of d. See https://doi.org/10.1101/240804 for more details.
Usage
1 | sHWE(X, LF, B)
|
Arguments
X |
a matrix of SNP genotypes, i.e. an integer matrix of 0's, 1's, and 2's. Sparse matrices of class Matrix are not supported (yet). |
LF |
matrix of logistic factors |
B |
number of null datasets to generate - B=1 is usualy sufficient. If computational time/power allows, a few extra B could be helpful |
Value
a vector of p-values for each SNP.
Examples
1 2 3 4 5 6 | LF <- lfa(hgdp_subset, 4)
gof_4 <- sHWE(hgdp_subset, LF, 3)
LF <- lfa(hgdp_subset, 10)
gof_10 <- sHWE(hgdp_subset, LF, 3)
hist(gof_4)
hist(gof_10)
|
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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