Last updated: 2019-06-12

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Knit directory: Comparative_eQTL/analysis/

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Rmd 7ef6fe2 Benjmain Fair 2019-06-11 update site
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Rmd f47ec35 Benjmain Fair 2019-04-25 updated site
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Rmd e592335 Benjmain Fair 2019-04-03 build site
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html 5b477a3 Benjmain Fair 2019-03-19 Build site.
Rmd b1207ee Benjmain Fair 2019-03-19 Start workflowr project.

Welcome to my research website.

QC

Association testing with various models

  • first iteration: description: lmm with KING-robust GRM thresholded at 0, and 3 genotype PCs
  • Check residuals after regressing out some covariates
  • second iteration: description: lm with 5 genotype PCs (PCs 4 and 5 takes into account some first hand relatedness) and more stringent genotype filtering. Also, outlier sample MD_And dropped from analysis
  • Third iteration
  • fourth iteration: description, lmm with 4 PCs and 3 Genotype PCs, used STAR RNA-seq CPM for less outliers. Fixed big bug that was permuting samples, resulting in no true hits in previous iterations. Here I used standardization and qqnorm.

Conservation and GO analysis

  • GO analysis, FDR=0.1 overlap enrichment analysis of eGenes across humans and chumps, and gene ontology analysis of eGenes based on eGene classification defined at FDR=0.1 threshold
  • Conservation analysis, FDR=0.1 analysis of conservation of coding sequence (percent identity and dN/dS) based on eGene classification defined at FDR=0.1
  • Conservation analysis, HumanTop600_eGenes analysis of conservation of coding sequence (percent identity and dN/dS) based on eGene classification defined at FDR=0.1 for chimp and top600 qvalue genes for human.