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jamesliley's Projects

cfdr icon cfdr

Implements conditional false-discovery rate hypothesis testing, used to perform high-dimensional hypothesis tests. Requires a set of summary statistics in an experiment of interest, and 'levers' on a second set of summary statistics at the same variables for a second experiment. Enables frequentist hypothesis testing with overall strong control of false-discovery rate. Can use several estimators of the cFDR function.

cfdr-common-controls icon cfdr-common-controls

This repository contains R functions to compute the 'Conditional False Discovery Rate', a method to analyse genome-wide association studies (GWAS) for related diseases originally proposed by Andreasson et al (2013), in the case where the two GWAS have shared controls.These functions widen the scope of the existing technique and enable improved power.

cfdr_control_pipeline icon cfdr_control_pipeline

Pipeline for generation of all plots and results in paper 'Accurate error control in high dimensional association testing using conditional false discovery rates' by James Liley and Chris Wallace (to be submitted)

cfdr_estimation_pipeline icon cfdr_estimation_pipeline

Pipeline for generation of all plots and results in paper 'New estimators for conditional false discovery rates improve power and smoothness' by James Liley and Chris Wallace (to be submitted)

cfdr_pipeline icon cfdr_pipeline

Pipeline to generate all results in manuscript 'Accurate error control in high dimensional association testing using conditional false discovery rates', by James Liley and Chris Wallace

dlai4 icon dlai4

Durham University MATH4267: Deep Learning and Artificial Intelligence

model_updating icon model_updating

Supporting code for manuscript 'Model updating after interventions paradoxically introduces bias'

optholdoutsize icon optholdoutsize

R package for estimation of optimal size of a 'holdout' set for planned updating of a predictive score

pea_risk icon pea_risk

Analysis of surgical risk in pulmonary endarterectomy (PEA).

sparrav4 icon sparrav4

Public repository for code used in manuscript on SPARRA version 4

subtest icon subtest

A package for testing for differential genetic basis between two putative disease subtypes.

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