Multi_Anno: Run Multi-Trait with Annotation Model

In JustinaXie/MDATA: Multi-trait for De novo mutation Association Test with Annotations

Description

Run Multi-Trait with Annotation Model

Usage

Multi_Anno(
  data,
  Anno1,
  Anno2,
  N_1,
  N_2,
  pi_init = c(0.85, 0.05, 0.05, 0.05),
  beta0_trait1_init,
  beta0_trait2_init,
  threshold_1 = 0.001,
  threshold_2 = 0.001,
  max_iter = 200
)

Arguments

data	A dataframe with columns: Gene name, mutability, de novo mutation count for trait1, de novo mutation count for trait2
Anno1	Annotation file for trait 1
Anno2	Annotation file for trait 2
N_1	Cohort size for trait 1
N_2	Cohort size for trait 2
pi_init	Initial value for probabilities of genes under different assumptions. Default=c(0.85,0.05,0.05,0.05)
beta0_trait1_init	Initial value for log gamma for trait 1
beta0_trait2_init	Initial value for log gamma for trait 2
threshold_1	Threshold for EM algorithm. Default=1e-3
threshold_2	Threshold for Newton's method. Default=1e-3
max_iter	Maximum iteration for Newton's method. Default=200

Value

The estimated model parameters and the posterior probabilities of genes under different assumptions

result	A dataframe that includes estimated posterior probabilities of risk genes for each trait and estimated posterior probability for shared risk gene
pi	Estimated proportion of genes under different assumptions
beta_trait1	Estimated beta vector for trait 1
beta_trait2	Estimated beta vector for trait 2
Z_mat	Estimated posterior probabilities of genes under different assumptions

JustinaXie/MDATA documentation built on Dec. 18, 2021, 2:34 a.m.