deletions | additions       diff --git a/Sensitivity analysis using previously identified eQTLs.tex b/Sensitivity analysis using previously identified eQTLs.tex  index 066e0cc..db8ed30 100644  --- a/Sensitivity analysis using previously identified eQTLs.tex  +++ b/Sensitivity analysis using previously identified eQTLs.tex 
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\subsubsection{Identifying known European eQTLs in 70 Yoruba LCLs}  We downloaded a a set of 1895 eQTLs which were identified in 462 European lymphoblastoid cell lines (LCLs) by the GEUVADIS project \cite{24037378}. We identified the subset of these eQTL SNPs that were segregating in an independent dataset of 69 Yoruba LCLs \cite{Stephens_Gilad_Pritchard_2010} with a minimum minor allele count of 2. We then applied the CHT and linear model to the RNA-seq data from the Yoruba LCLs. % TODO: say something about As target  regions for each test we  used (i.e. exons) the set of non-redundant Ensembl exons from the associated gene.  \subsubsection{Genome-wide QTL discovery in small sample sizes of ChIP-seq data}  We also applied the two models to a dataset of ChIP-seq data for the histone modification H3K27ac on 10 individuals, which we collected in a previous study \cite{McVicker_2013}. Principle components were not included in this analysis because of the small number of dimensions in the dataset. % TODO say something about target regions As test SNPs we chose SNPs that were segregating in the 10 individuals  and filtering of defined the target region as a 2kb region centered on the test SNP. We only tested target  regions prior to applying test... with at least 100 filtered reads (summed across individuals).