3.1 Compute variant-based and gene-based segregation information for different mode of inheritance. | 3.2 Compute gene-based segregation test. | 3.3 Compute the weighted gene-based segregation test. | 3.4. Other useful methods | 3.4.1. Trimming the pedigree file | 3.4.2. Compute the conditional segregating probability
Package: GESE 2.0.1
Dandi Qiao
GESE: Gene-Based Segregation Test
Implements the gene-based segregation test(GESE) and the weighted GESE test for identifying genes with causal variants of large effects for family-based sequencing data. The methods are described in Qiao, D. Lange, C., Laird, N.M., Won, S., Hersh, C.P., et al. (2017). <doi:10.1002/gepi.22037>. Gene-based segregation method for identifying rare variants for family-based sequencing studies. Genet Epidemiol 41(4):309-319. More details can be found at <http://scholar.harvard.edu/dqiao/gese>.
Authors:
GESE_2.0.1.tar.gz
GESE_2.0.1.tar.gz(r-4.7-any)GESE_2.0.1.tar.gz(r-4.6-any)
GESE_2.0.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
GESE/json (API)
| # Install 'GESE' in R: |
| install.packages('GESE', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated from:3de6049749. Checks:2 WARNING, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | WARNING | 169 | ||
| source / vignettes | OK | 219 | ||
| linux-release-x86_64 | WARNING | 145 | ||
| wasm-release | OK | 113 |
Exports:condSegProbFGESEgetSegInfotrim_oneLineagetrim_unrelated
Dependencies:evaluatehighrkinship2knitrlatticeMatrixquadprogxfunyaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Gene-Based Segregation Test | GESE-package |
| Computes conditional segregation probability for the family | condSegProbF |
| database file in example | database |
| dataRaw - a data frame containing the pedigree, phenotype and genotype information | dataRaw |
| Gene-Based Segregation Test | GESE |
| GESE package internal functions | GESE-internal functions |
| Computes segregation information for different mode of inheritance. | getSegInfo |
| mafInfo - example data | mapInfo |
| pednew - an example pedigree structure | pednew |
| Trims the pedigree structure to include one lineage only. | trim_oneLineage |
| Trims the pedigree structure to exclude multiple founder cases | trim_unrelated |