Single_Anno: Run Single-Trait with Annotation Model

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

Description

Run Single-Trait with Annotation Model

Usage

Single_Anno(
  data,
  dn_col,
  N_1,
  Anno,
  pi_init = 0.1,
  beta0_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 traits
dn_col	A character indicating the column name of de novo mutation counts for the trait
N_1	Cohort size for the trait
Anno	Annotation file for the trait
pi_init	Initial value for risk gene proportion. Default=0.1
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 vector, the second value represents risk gene proportion
beta	Estimated beta vector
Z_mat	Estimated posterior probabilities of genes under different assumptions

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