ASE_detection.Rd
This function is used to detect ASE genes under one condition given bulk RNA-seq data that may contain multiple genes.
ASE_detection( dat_all, phased = FALSE, varList = NULL, adaptive = TRUE, n_resample = 10^6, parallel = FALSE, n_core = 1, save_out = FALSE, name_out = NULL )
dat_all: | bulk RNA-seq data. Must contain variables:
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phased: | a logical value indicates whether the haplotype phase of the data is known or not. Default is FALSE |
varList: | a character string specifies fomula 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 |
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 paramter "parallel" is set to TRUE. Default is 1 |
save_out: | a logical value indicates whether to write out the result for each gene stepwisely to a txt file. Default is FALSE |
name_out: | a character string indicates the output file name when save_out is set to TRUE, with the format of "XXX.txt" |
A matrix with three columns:
`gene`: character, gene name;
`p-value`: the estimated p-value of the likelihood ratio test (LRT) statistic;