README file:

Read me for GEUVADIS_replication.RData file

The expression data in this workspace was produced by the GEUVADIS consortium and published in Lappalainen et al. 2013. Transcriptome and genome sequencing uncovers functional variation in humans. Nature, 501, 506-11.

Genotype objects:

het: posterior probability of being a het for v-eQTL and epistasis SNPs
hom: posterior probability of being a hom for v-eQTL and epistasis SNPs
dose: dosage for v-eQTL and epistasis SNPs
eqtl.dosage: dosage of all significant eQTL

Expression objects:

expr: expression values for all genes

Covariates:

cov: covariate matrix listing populations for all individuals
cov.p: factor, used in regression models to control for population effects

Results files:

vQTL: vQTL results in TwinsUK and replication evidence in GEUVADIS
epistasis: All significant epistatic hits in TwinsUK and replication evidence in GEUVADIS
eqtl.list: List of all independently significant eQTL for the 131 genes with statistical replication in GEUVADIS dataset

Functions:

VqtlFunction: Applied to row of vQTL, calculates the replication p value in GEUVADIS, e.g. VqtlFunction(vQTL[1, ]) = 0.0250845 = vQTL[1, 9]
EpistasisFunction: Applied to row of epistasis, returns the additive variance explained, interactions variance explained, and the replication p value for interactions in GEUVADIS, e.g. EpistasisFunction(epistasis[1, ]) = 3.102766e-01 -1.277897e-01  5.425824e-22 = epistasis[1, 8:10]
EqtlControl: Given an interaction with statistical replication in GEUVADIS, it calculates evidence of interactions conditional on all eQTL and reports the least significant, e.g. EqtlControl(epistasis[1,]) = 4.694224e-06 = epistasis[1, 11]