Get_DE_geneinfor: Difference expression analysis

In NWPU-903PR/m6Aexpress: Predicting context-specific m6A regulation of gene expression

Description

Obtain the differential gene information and sequence library size facor by DESeq2

Usage

Select_DEgene(gene_count_infor,
              cond1, 
              cond2,
              num_cond1, 
              num_cond2,
              DIFF_GENE_CUTOFF_PVALUE=0.05,
              DIFF_GENE_cutoff_FDR=0.05,
              DE_CUTOFF_TYPE="padj")

Arguments

gene_count_infor	A list data format, which includes a dataframe quantified the gene expression with reads count for each gene in each sample under specific context and a vector of size factor to normalize gene expression of INPUT samples in the furture.
cond1	A string,such as "control", which specifices the name for the one condition.
cond2	A integer,such as "treated", which specifices the name for the second condition.
num_cond1	A integer,such as "2", which specifices the number of samples in the one condition.
num_cond2	A integer,such as "2", which specifices the number of samples in the second condition.
DIFF_GENE_CUTOFF_PVALUE	A decimal number, which specifies the p-value cut-off to identify differential expression gene in DESeq2 R-package, default: 0.05.
DIFF_GENE_cutoff_FDR	A decimal number, which specifies the fdr cut-off to identify differential expression gene in DESeq2 R-package, default: 0.05.
DE_CUTOFF_TYPE	A string, such as "padj", which specifies the tpye of cut-off to identify differential expression gene, default: DE_CUTOFF_TYPE="padj".

Details

This function is to identify different expresseion gene by DESeq2 and return reads count for different expression (DE) gene, library size factor for further sample normalization and DE gene information, such as "log2foldchange", "p-value","padj".

Value

This function will return a list including reads count for DE gene, size facor and DE gene information.

DE_gene_count	A dataframe, which includes the reads count of DE gene for samples under two specific conditions.
size_factor	A vector in float type, which are used to normalize samples.
significant_DE_gene	A dataframe format, which includes the DE gene information.

References

Love, M.I., Huber, W., Anders, S. (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology, 15:550. https://doi.org/10.1186/s13059-014-0550-8

Examples

## Not run: 
##get reads count for each gene
get_gene_express <- Get_express_data(INPUT_BAM=INPUT_BAM, 
                                      isPairedEnd=FALSE,
                                      GENE_ANNO_GTF = gtf)
##do the DE analysis
obtain_DEgene <- Select_DEgene(gene_count_infor=get_gene_express,
                               cond1="control", 
                               cond2="treated",
                               num_cond1=2, 
                               num_cond2=2,
                               DIFF_GENE_CUTOFF_PVALUE=0.05,
                               DIFF_GENE_cutoff_FDR=0.05,
                               DE_CUTOFF_TYPE="padj") 

## End(Not run)

NWPU-903PR/m6Aexpress documentation built on Dec. 17, 2021, 5:18 a.m.