obtain_gene_expression: Obtain gene expression

In NWPU-903PR/m6AexpressBHM: m6Aexpress-BHM: Predicting m6A regulation of gene expression in multiple-groups context by a Bayesian Hierarchical Mixture model

Obtain gene expression

Description

Obtain the reads count for each gene to represent the expression of each gene and report the sequencing depth size factors for each Input samples

Usage

obtain_gene_expression(Input_data, 
                       GTF_file, 
                       nthreads=1, 
                       isPairedEnd=FALSE,
                       Group_label,
                       rep_num)

Arguments

Input_data	a character vector for the BAM file directories of the Input samples, which are used to quantify gene expression.
GTF_file	a character specifies the directory toward a gene annotation GFF/GTF file.
nthreads	a integer giving the number of threads used for running this function. 1 by default.
isPairedEnd	a logical scalar or a logical vector, indicating whether libraries contain paired-end reads or not. FALSE by default.
Group_label	a character vector giving the name of each concerned group.
rep_num	a integer vector giving the number samples of each concerned group.

Value

It will return a list containing two components:

gene_express	a matrix including gene reads count in each sample of each concerned group
size_factor	a numeric vector specifying the sequencing depth size factors for each Input samples.

Examples

## Not run: 
### obtain gene reads count from Input dataset in BAM format
Input_data <- c(group1_INPUT_BAM,group2_INPUT_BAM,group3_INPUT_BAM)
gene_expression <- obtain_gene_expression(Input_data=Input_data, 
                                          GTF_file=GENE_ANNO_GTF, 
                                          nthreads=10, 
                                          isPairedEnd=FALSE,
                                          Group_label=c("Group1","Group2","Group3"),
                                          rep_num=c(3,3,3))

## End(Not run)

NWPU-903PR/m6AexpressBHM documentation built on May 29, 2022, 11:07 p.m.