AffiXcan-package: A functional approach to impute GReX

In AffiXcan: A Functional Approach To Impute Genetically Regulated Expression

Description

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) score. Statistical models to impute GReX can be trained on a training dataset where the real total expression values are known.

Details

For every gene a linear regression model can be fitted on a training set of individuals where the real total expression values, the Total Binding Affinity (TBA) values for a set of genomic regions, and the covariates of the population genetic structure, are known. AffiXcan performs a principal component analysis (PCA) on the TBA values to fit a linear model using the formula: GReX ~ PC1 + PC2 + PC3 + ... + COV1 + COV2 + ... . Associations between the expressed genes and the regulatory regions, on which the TBA values have to be computed, are needed. TBA can be computed using "vcf_rider" software (see references)

Author(s)

Alessandro Lussana <[e-mail]> Maintainer: Alessandro Lussana <[e-mail]>

References

https://github.com/vodkatad/vcf_rider

Examples

trainingTbaPaths <- system.file("extdata","training.tba.toydata.rds",
package="AffiXcan")

data(exprMatrix)
data(regionAssoc)
data(trainingCovariates)

assay <- "values"

training <- affiXcanTrain(exprMatrix=exprMatrix, assay=assay,
tbaPaths=trainingTbaPaths, regionAssoc=regionAssoc, cov=trainingCovariates,
varExplained=80, scale=TRUE)

testingTbaPaths <- system.file("extdata","testing.tba.toydata.rds",
package="AffiXcan")

exprmatrix <- affiXcanImpute(tbaPaths=testingTbaPaths, affiXcanTraining=training,
scale=TRUE)

AffiXcan documentation built on Nov. 8, 2020, 8:07 p.m.