Package: wISAM 0.2.8
wISAM: Weighted Inbred Strain Association Mapping
In the course of a genome-wide association study, the situation often arises that some phenotypes are known with greater precision than others. It could be that some individuals are known to harbor more micro-environmental variance than others. In the case of inbred strains of model organisms, it could be the case that more organisms were observed from some strains than others, so the strains with more organisms have better-estimated means. Package 'wISAM' handles this situation by allowing for weighting of each observation according to residual variance. Specifically, the 'weight' parameter to the function conduct_scan() takes the precision of each observation (one over the variance).
Authors:
wISAM_0.2.8.tar.gz
wISAM_0.2.8.zip(r-4.5)wISAM_0.2.8.zip(r-4.4)wISAM_0.2.8.zip(r-4.3)
wISAM_0.2.8.tgz(r-4.4-any)wISAM_0.2.8.tgz(r-4.3-any)
wISAM_0.2.8.tar.gz(r-4.5-noble)wISAM_0.2.8.tar.gz(r-4.4-noble)
wISAM_0.2.8.tgz(r-4.4-emscripten)wISAM_0.2.8.tgz(r-4.3-emscripten)
wISAM.pdf |wISAM.html✨
wISAM/json (API)
| # Install 'wISAM' in R: |
| install.packages('wISAM', repos = c('https://rcorty.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/rcorty/wisam/issues
- covariate_mat - Example covariate matrix
- kinship_mat - Example kinship matrix
- locus_list - Example locus list
- phenotype - Example phenotype
- se_mean_per_strain - Example standard error of the mean per strain
geneticsgwasgwas-toolslmmmixed-models
Last updated 6 years agofrom:9d90e9d810. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 21 2024 |
| R-4.5-win | NOTE | Nov 21 2024 |
| R-4.5-linux | NOTE | Nov 21 2024 |
| R-4.4-win | NOTE | Nov 21 2024 |
| R-4.4-mac | NOTE | Nov 21 2024 |
| R-4.3-win | NOTE | Nov 21 2024 |
| R-4.3-mac | NOTE | Nov 21 2024 |
Exports:check_eigen_decompositionGenomeScan
Dependencies:MASS
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| check_eigen_decomposition | check_eigen_decomposition |
| Example covariate matrix | covariate_mat |
| calc_multiplier_eigen | GenomeScan_calc_multiplier_eigen |
| conduct_scan | GenomeScan_conduct_scan |
| fit_locus | GenomeScan_fit_locus |
| fit_locus_given_h2 | GenomeScan_fit_locus_given_h2 |
| initialize | GenomeScan_initialize |
| prep_scan | GenomeScan_prep_scan |
| GenomeScan | GenomeScan GenomeScan-class |
| Example kinship matrix | kinship_mat |
| Example locus list | locus_list |
| Example phenotype | phenotype |
| Example standard error of the mean per strain | se_mean_per_strain |
