GESE: Gene-Based Segregation Test

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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., Hobbs, B., et al. 2016. Gene-based segregation method for identifying rare variants for family-based sequencing studies. More details can be found at <http://scholar.harvard.edu/dqiao/gese>.

Author
Dandi Qiao, Michael H. Cho
Date of publication
2016-11-16 23:56:52
Maintainer
Dandi Qiao <redaq@channing.harvard.edu>
License
GPL-2
Version
2.0.0

View on CRAN

Man pages

condSegProbF
Computes conditional segregation probability for the family
database
database file in example
dataRaw
dataRaw - a data frame containing the pedigree, phenotype and...
GESE
Gene-Based Segregation Test
GESE-internal
GESE package internal functions
GESE-package
\Sexpr[results=rd,stage=build]{tools:::Rd_package_title("GESE")}
getSegInfo
Computes segregation information for different mode of...
mapInfo
mafInfo - example data
pednew
pednew - an example pedigree structure
trim_oneLineage
Trims the pedigree structure to include one lineage only.
trim_unrelated
Trims the pedigree structure to exclude multiple founder...

Files in this package

GESE
GESE/inst
GESE/inst/doc
GESE/inst/doc/my-vignette.Rmd
GESE/inst/doc/my-vignette.R
GESE/inst/doc/my-vignette.pdf
GESE/NAMESPACE
GESE/data
GESE/data/mapInfo.rda
GESE/data/dataRaw.rda
GESE/data/pednew.rda
GESE/data/database.rda
GESE/R
GESE/R/getProb_weight.R
GESE/R/getSegInfo.R
GESE/R/findIntermediateFounder.R
GESE/R/condSegProbF.R
GESE/R/findMostRecentCommonFounderControl.R
GESE/R/getTranProb_dv.R
GESE/R/getProb.R
GESE/R/GESE.R
GESE/R/getPvalue_resampling.R
GESE/R/trim_oneLineage.R
GESE/R/trim_unrelated.R
GESE/R/getFounder.R
GESE/R/findMostRecentCommonFounder.R
GESE/R/computeP_resampling.R
GESE/R/oneSetSim.R
GESE/R/segProb.R
GESE/R/isRelated.R
GESE/vignettes
GESE/vignettes/my-vignette.Rmd
GESE/MD5
GESE/build
GESE/build/vignette.rds
GESE/build/partial.rdb
GESE/DESCRIPTION
GESE/man
GESE/man/trim_oneLineage.Rd
GESE/man/GESE.Rd
GESE/man/GESE-internal.Rd
GESE/man/getSegInfo.Rd
GESE/man/GESE-package.Rd
GESE/man/pednew.Rd
GESE/man/database.Rd
GESE/man/mapInfo.Rd
GESE/man/dataRaw.Rd
GESE/man/trim_unrelated.Rd
GESE/man/condSegProbF.Rd