one_condition_analysis_Gene: Perform ASE analysis in the population for a given gene

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

Description

This function is used to perform ASE detection for one condition analysis of a given gene.

Usage

one_condition_analysis_Gene(
  dat,
  phased = FALSE,
  varList = NULL,
  n_resample = 10^6,
  adaptive = TRUE,
  parallel = FALSE,
  n_core = 1
)

Arguments

dat:	bulk RNA-seq data of a given gene. Must contain variables: 'id': character, individual identifier; 'ref': numeric, the snp-level read counts for the reference allele if the haplotype phase of the data is unknown, and the snp-level read counts for allele aligned on paternal/maternal haplotype if haplotype phase is known; 'total': numeric, snp-level total read counts for both alleles;
phased:	a logical value indicates whether the haplotype phase of the data is known or not. Default is FALSE
varList:	a character string specifies formula of covariates that users want to adjusted in the model. An example could be "'var1'+'var2'". Default is NULL
n_resample:	a numeric value indicates the maximum number of resamplings performed to obtain estimated p-value. Default is 10^6
adaptive:	a logical value indicates whether the resampling is done through an adaptive procedure or not. Only applies when n_resample >= 10^3. Default is TRUE By adaptive, it means first do 1000 resamplings, if the estimated p-value < 0.1, increase the number of resampling, by a factor of 10, to 10^4. if then the estimated p-value < 0.01, increase the number of resampling again, by a factor of 10, to 10^5. The procedure continuous until reaches the maximum number of resampling.
parallel:	a logical value indicates whether do parallel computing for the resampling precedure or not. Default is FALSE
n_core:	a numeric value indicates number of clusters used for parallel computing when parameter "parallel" is set to TRUE. Default is 1

Value

A vector with two elements:

• 'LRT statistic': numeric, the likelihood ratio test (LRT) statistics of ASE effect;

• 'p-value': the estimated p-value of the LRT statistic;

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