Package: INTACT 1.5.0
INTACT: Integrate TWAS and Colocalization Analysis for Gene Set Enrichment Analysis
This package integrates colocalization probabilities from colocalization analysis with transcriptome-wide association study (TWAS) scan summary statistics to implicate genes that may be biologically relevant to a complex trait. The probabilistic framework implemented in this package constrains the TWAS scan z-score-based likelihood using a gene-level colocalization probability. Given gene set annotations, this package can estimate gene set enrichment using posterior probabilities from the TWAS-colocalization integration step.
Authors:
INTACT_1.5.0.tar.gz
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INTACT.pdf |INTACT.html✨
INTACT/json (API)
NEWS
# Install 'INTACT' in R: |
install.packages('INTACT', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/jokamoto97/intact/issues
- exprwt_sumstats - TWAS weights for a simulated gene.
- gene_set_list - Simulated gene set list.
- ld_sumstats - LD correlation matrix from a simulated data set.
- multi_simdat - Simulated TWAS, PWAS, and pairwise colocalization summary data.
- protwt_sumstats - PWAS weights for a simulated gene.
- simdat - Simulated TWAS and colocalization summary data.
- z_sumstats - TWAS and PWAS z-score for a simulated gene.
On BioConductor:INTACT-1.5.0(bioc 3.20)INTACT-1.4.0(bioc 3.19)
Last updated 2 months agofrom:cb10773dc1
Exports:chisq_sumstatexpitfdr_rsthybridintactintactGSElinearmulti_intactstep
Dependencies:bdsmatrixclicpp11dplyrfansigenericsgluelifecyclemagrittrnumDerivpillarpkgconfigpurrrR6rlangSQUAREMstringistringrtibbletidyrtidyselectutf8vctrswithr