seqMeta: Meta-Analysis of Region-Based Tests of Rare DNA Variants
Version 1.6.7

Computes necessary information to meta analyze region-based tests for rare genetic variants (e.g. SKAT, T1) in individual studies, and performs meta analysis.

Browse man pages Browse package API and functions Browse package files

AuthorArie Voorman, Jennifer Brody, Han Chen, Thomas Lumley, Brian Davis
Date of publication2017-02-09 15:24:14
MaintainerBrian Davis <Brian.Davis281@gmail.com>
LicenseGPL (>= 2)
Version1.6.7
URL https://github.com/DavisBrian/seqMeta
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("seqMeta")

Man pages

burdenMeta: Meta analyze burden tests from multiple studies
prepCondScores: Run SKAT on data from a single cohort, conditional on...
prepScores: Prepare scores for region based (meta) analysis
prepScores2: Prepare scores for region based (meta) analysis
seqMeta: seqMeta: Meta-Analysis of Region-Based Tests of Rare DNA...
seqMetaExample: Example data for illustrating seqMeta
singlesnpMeta: Meta analyze single snp effects from multiple studies
skatMeta: Combine SKAT analyses from one or more studies
skatOMeta: Combine SKAT-O analyses from one or more studies.
SNPInfo: Illumina HumanExome BeadChip SNP Information file

Functions

SNPInfo Man page
Z1 Man page
Z2 Man page
burdenMeta Man page Source code
c.seqMeta Source code
c.skatCohort Source code
calculate_cov Source code
calculate_maf Source code
check_dropped_subjects Source code
check_format_skat Source code
check_inputs Source code
coxlr.fit Source code
create_model Source code
create_seqMeta Source code
fill_values Source code
getcc Source code
ginv_s Source code
impute_to_mean Source code
is.family Source code
is_mono Source code
is_monomorphic Source code
kins Man page
monomorphic_snps Source code
pchisqsum2 Source code
pheno1 Man page
pheno2 Man page
prepCondScores Man page Source code
prepCox Man page Source code
prepGenotype Source code
prepSNPInfo Source code
prepScores Man page Source code
prepScores2 Man page Source code
prepScoresX Man page Source code
saddle Source code
seqMeta Man page
seqMeta-package Man page
seqMetaExample Man page
singlesnpMeta Man page Source code
skatMeta Man page Source code
skatOMeta Man page Source code
skatO_getp Source code

Files

inst
inst/doc
inst/doc/seqMeta.Rnw
inst/doc/seqMeta.R
inst/doc/seqMeta.pdf
tests
tests/testthat.R
tests/testthat
tests/testthat/test-prepSNPInfo.R
tests/testthat/test-prepScores2.R
tests/testthat/test-examples.R
tests/testthat/test-bugfixes.R
tests/testthat/test-issue2.R
tests/testthat/test-issue1.R
src
src/chinv2.c
src/survS.h
src/chsolve2.c
src/survproto.h
src/coxfit6.c
src/cholesky2.c
src/coxsafe.c
src/dmatrix.c
NAMESPACE
NEWS.md
data
data/SNPInfo.rda
data/seqMetaExample.rda
data/datalist
R
R/pchisqsum2.R
R/utils.R
R/prepAdjust.R
R/c.seqMeta.R
R/burdenMeta.R
R/seqMeta.R
R/check_format_skat.R
R/singlesnpMeta.R
R/coxlr.fit.R
R/skatOMeta.R
R/prepScores2.R
R/prepCox.R
R/skatMeta.R
R/prepScores.R
vignettes
vignettes/seqMeta.Rnw
README.md
MD5
build
build/vignette.rds
DESCRIPTION
man
man/seqMetaExample.Rd
man/singlesnpMeta.Rd
man/burdenMeta.Rd
man/prepScores2.Rd
man/SNPInfo.Rd
man/prepScores.Rd
man/prepCondScores.Rd
man/seqMeta.Rd
man/skatMeta.Rd
man/skatOMeta.Rd
seqMeta documentation built on May 20, 2017, 12:03 a.m.