Package: MAPITR 1.1.2

Michael Turchin

MAPITR: MArginal ePIstasis Test for Regions

A genetic analysis tool and variance component model for identifying marginal epistasis between pathways and the rest of the genome. 'MAPITR' uses as input a matrix of genotypes, a vector of phenotypes, and a list of pathways. 'MAPITR' then iteratively tests each pathway for epistasis between any variants within the pathway versus any variants remaining in the rest of the genome. 'MAPITR' returns results in the form of p-values for every pathway indicating whether the null model of there being no epistatic interactions between a pathway and the rest of the genome can be rejected.

Authors:Michael Turchin [aut, cre], Gregory Darnell [aut, ctb], Lorin Crawford [aut, ctb], Sohini Ramachandran [aut], Peter Carbonetto [ctb]

MAPITR_1.1.2.tar.gz
MAPITR_1.1.2.tar.gz(r-4.5-noble)MAPITR_1.1.2.tar.gz(r-4.4-noble)
MAPITR_1.1.2.tgz(r-4.4-emscripten)MAPITR_1.1.2.tgz(r-4.3-emscripten)
MAPITR.pdf |MAPITR.html
MAPITR/json (API)

# Install 'MAPITR' in R:
install.packages('MAPITR', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/mturchin20/mapitr/issues

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
  • openmp– GCC OpenMP (GOMP) support library
Datasets:

openblascppopenmp

2.70 score 152 downloads 1 exports 7 dependencies

Last updated 4 years agofrom:b3656a0912. Checks:OK: 1 NOTE: 1. Indexed: no.

TargetResultDate
Doc / VignettesOKDec 11 2024
R-4.5-linux-x86_64NOTEDec 11 2024

Exports:MAPITR

Dependencies:codetoolsCompQuadFormdoParallelforeachiteratorsRcppRcppArmadillo

MAPITR Introduction -- Simulated Data

Rendered fromMAPITR.Intro.SimulatedData.Rmdusingknitr::rmarkdownon Dec 11 2024.

Last update: 2020-09-23
Started: 2020-09-17

Readme and manuals

Help Manual

Help pageTopics
MArginal ePIstasis Test for Regions ('MAPITR')MAPITR
MAPITR SimData GenotypesMAPITR_SimData_Genotypes
MAPITR SimData PathwaysMAPITR_SimData_Pathways
MAPITR SimData PCsMAPITR_SimData_PCs
MAPITR SimData PhenotypeMAPITR_SimData_Phenotype
MAPITR TestData GenotypesMAPITR_TestData_Genotypes
MAPITR TestData PathwaysMAPITR_TestData_Pathways
MAPITR TestData PCsMAPITR_TestData_PCs
MAPITR TestData PhenotypeMAPITR_TestData_Phenotype