Package: AffiXcan 1.25.0

Alessandro Lussana

AffiXcan: A Functional Approach To Impute Genetically Regulated Expression

Impute a GReX (Genetically Regulated Expression) for a set of genes in a sample of individuals, using a method based on the Total Binding Affinity (TBA). Statistical models to impute GReX can be trained with a training dataset where the real total expression values are known.

Authors:Alessandro Lussana [aut, cre]

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AffiXcan.pdf |AffiXcan.html✨
AffiXcan/json (API)
NEWS

# Install 'AffiXcan' in R:

install.packages('AffiXcan', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

exprMatrix - Expression data of two genes for 229 individuals
regionAssoc - Associations between regulatory regions and expressed genes
trainingCovariates - Covariates of the population structure for 229 individuals

On BioConductor:AffiXcan-1.25.0(bioc 3.21)AffiXcan-1.24.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

geneexpression transcription generegulation dimensionreduction regression principalcomponent

4.00 score 328 downloads 15 exports 58 dependencies

Last updated 2 months agofrom:091b100ef6. Checks:OK: 1 NOTE: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 29 2024
R-4.5-win	NOTE	Nov 29 2024
R-4.5-linux	NOTE	Nov 29 2024
R-4.4-win	NOTE	Nov 29 2024
R-4.4-mac	NOTE	Nov 29 2024
R-4.3-win	NOTE	Nov 29 2024
R-4.3-mac	NOTE	Nov 29 2024

Exports:affiXcanBs affiXcanGReX affiXcanImpute affiXcanPca affiXcanPcs affiXcanTrain assoc2list computeBs computeCorrelation computeExpr computePca computePcs computeRSquared overlookRegions subsetKFold

Dependencies:abind askpass BH Biobase BiocBaseUtils BiocGenerics BiocParallel cli codetools cpp11 crayon curl DelayedArray dplyr fansi formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicRanges glue httr IRanges jsonlite lambda.r lattice lifecycle magrittr Matrix MatrixGenerics matrixStats mime MultiAssayExperiment openssl pillar pkgconfig purrr R6 rlang S4Arrays S4Vectors snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect UCSC.utils utf8 vctrs withr XVector zlibbioc

AffiXcan

Alessandro Lussana

Rendered fromAffiXcan.Rmdusingknitr::rmarkdownon Nov 29 2024.

Last update: 2019-10-13
Started: 2018-09-04

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
A functional approach to impute GReX	AffiXcan-package AffiXcan
Fit linear models and compute ANOVA p-values	affiXcanBs
Compute a GReX from variables and their coefficients for a set of genes	affiXcanGReX
Impute a GReX for each gene for which a model was generated	affiXcanImpute
Perform a PCA on each experiment found in MultiAssayExperiment objects	affiXcanPca
Compute PCs in MultiAssayExperiment objects using eigenvectors given by user	affiXcanPcs
Train the model needed to impute a GReX for each gene	affiXcanTrain
Reorganize associations table in a list	assoc2list
Fit a linear model to impute a GReX for a certain gene	computeBs
Compute R and R^2 on a particular row of two SummarizedExperiment assays	computeCorrelation
Compute the imputed GReX for a certain gene on a set of individuals	computeExpr
Perform a PCA on a matrix where columns are variables	computePca
Compute a matrix product between variables and eigenvectors	computePcs
Compute R and R^2 between rows of two SummarizedExperiment assays	computeRSquared
Expression data of two genes for 229 individuals	exprMatrix
Count the number of genomic regions on which the TBA was computed	overlookRegions
Associations between regulatory regions and expressed genes	regionAssoc
Split the numbers from 1 to n in k equally-sized lists	subsetKFold
Covariates of the population structure for 229 individuals	trainingCovariates