modelFit: Model Fitting

In Jiaxin-Fan/ASEP: ASEP: Gene-based detection of allele-specific expression in a population by RNA seqencing

Description

This function is used to fit the generalized linear mixed-effect model through nonparametric maximum likelihood estimation for a given gene.

Usage

modelFit(
  dat_phase,
  n_condition = "one",
  resampled_data = FALSE,
  varList = NULL
)

Arguments

dat_phase:	Psudo-phased bulk RNA-seq data of a given gene
n_condition:	a character string indicates whether to perform one condition analysis or two conditions analysis. Possible values are "one" or "two". Default is "one"
resampled_data:	a logical value indicates whether the data analyzed is obtained from resampling or not. Used only for two conditions analysis. Default is FALSE
varList:	a character string specifies fomula of covariates that users want to adjusted in the model, e.g., "'var1'+'var2'". Default is NULL

Value

• One condition analysis: likelihood ratio test (LRT) statistic;
  

• Two conditions analysis:
  - original data: estimated ASE effect in the pooled sample & likelihood ratio test (LRT) statistic;
  - resampled data: likelihood ratio test (LRT) statistic;
  

Jiaxin-Fan/ASEP documentation built on Aug. 9, 2021, 6:39 a.m.