Description Details Author(s) References Examples

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.

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)

Alessandro Lussana <alessandro.lussana@protonmail.com> Maintainer: Alessandro Lussana <alessandro.lussana@protonmail.com>

https://github.com/vodkatad/vcf_rider

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 | ```
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.

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