-geneexpfile
Path to the file where the gene expression profile file is placed. For example:
-profile_path /home/user/profile/gene_expression/gene_exp_profile.txt
-num_ee_genes
The number of equivalently expressed (EE) genes between cases and controls. For example:
-num_ee_genes 100
-num_de_genes
The number of differentially expressed (DE) genes between cases and controls. For example:
-num_de_genes 100
Related options: -fc
-fc
The fold changes for the DE genes. For example:
-fc 2,3,1.5,1.5
The fold changes for the first, second, third, and fourth DE genes will be 2, 3, 1.5, and 1.5, respectively.
--no-shuffle
By default, gene profiles (i.e., the mean and dispersion parameter for a negative binomial distribution) are sampled with replacement for simulating the RNA-seq data. With this option, OmicsSIMLA will simulate the RNA-seq data according to the gene expression profiles without sampling. Hence, the simulated RNA-seq data will correspond to the same order of gene profiles in the file. Note that when this option is specified, the total number of genes simulated should not exceed the number of gene profiles in the gene expression profile file.