other code under posts

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01.Heritability_Sparsity

First…
Feb 7, 2022
natasha.santhanam

 

01.Heritability_Sparsity Sabrina

For each gene, we calculate heritability from its local GRM. Start with creating list of genes for each of the gene expression file:
Feb 7, 2022
natasha.santhanam , Sabrina

 

  1. Prediction_Model_Pipeline

Data from here - genoGex.Rdata has everything we need in it There are 5 ‘gex’ RDS…
Feb 7, 2022
Tyson Miller

 

03.PrediXcan_MultiXcan

Sabrina’s note: I have no idea what is going on here, I don’t know where bimbam file came from. I tried running this script from genotype files generated from previous steps…
Feb 7, 2022
Natasha Santhanam

 

04.GEMMA_LMM_analysis

Gemma uses a LMM with…
Apr 21, 2022
Natasha Santhanam

 

06.PTRS_Creation

The orth.rats file contains gives a dictionary between human genes and the corresponding gene in rats.
Feb 7, 2022
Natasha Santhanam

 

07 SPTRS_Creation

Set up the conda environment
Feb 7, 2022
Natasha Santhanam

 

08.Compare_all_PTRS

Match genes in weights file in humans to Rat expression
Feb 7, 2022
Natasha Santhanam

 

09.PRS_Rats

first extract out 500 random rats that we’ll use as baseline
May 4, 2022
Natasha Santhanam

 

10.PTRS_simulation_weights

Read in files
Jun 26, 2022
Natasha Santhanam

 

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Coregulation_across_Tissues_Species

Generate Correlation Matrices for 100 rats - compare predicted Expression across tissues
Feb 14, 2022
Natasha Santhanam

 

GTEx_comparison_rat_n_genes

Gather Genotype, Gene epression data, snp annotation file and gtf (made with ensembl notation)
Feb 14, 2022
Natasha Santhanam

 

Generate Sparsity Figures

we will use this for comparison later
Mar 9, 2022
Natasha Santhanam

 

Generate_plink_format_genotypes

Data from here - genoGex.Rdata has everything we need in it There are 5 ‘gex’ RDS…
Feb 14, 2022
Natasha Santhanam

 

Human_PTRS_Performance_Comparison

Yanyu’s PTRS weights estimate the effect of genes on a given trait, in this case we pick height and BMI.
Feb 24, 2022
Natasha Santhanam

 

PhenomeXcan Query

Generate a table of all human MultiXcan results
Feb 14, 2022
Natasha Santhanam

 

Rat QC and Comparison Check

Apurva sent bimbam files that I converted to map/ped and then bim/bed/fam files using my own pipeline. Pipeline is in rat_compare_genotypes_metabolic.Rmd file.
Feb 14, 2022
Natasha Santhanam

 

Rat_Predictability_comp_Humans

#Figure comparing pred R2 vs obs R2 in Ac tissue in Rats
Feb 14, 2022
Natasha Santhanam

 

Sparsity_Badger_Template

Feb 7, 2022
natasha.santhanam

 

convert_genotypes_old

Note: This is old script to convert Palmer lab genotype data in an .Rdata object to plink format. For our analysis, we used a different process to reformat, documented here
Feb 21, 2022

 

rat_compare_genotypes

Min. 1st Qu. Median Mean 3rd Qu. Max. 0.6856 0.7511 0.7851 0.7833 0.8211 0.8801
Feb 14, 2022
Natasha Santhanam
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