GSE66705_sample2        a matrix of gene expression data in GEO
Merge_methy_tcga        Merge methylation data downloaded from TCGA
ann_merge               Merge the copy number variation data downloaded
                        from TCGA using gdc
cal_mean_module         Find the mean value of the gene in each module
classify_sample         Get the differentially expressioned genes using
                        DESeq2 package
countToFpkm_matrix      Convert count to FPKM
countToTpm_matrix       Convert count to Tpm
diff_gene               Get the differentially expressioned genes using
                        DESeq2 package
differential_cnv        Do chi-square test to find differential genes
fpkmToTpm_matrix        Convert fpkm to Tpm
geneExpress             a data.frame of gene expression data
gene_ave                Average the values of same genes in gene
                        expression profile
hgnc                    a matrix for Converting gene symbol to
                        entrez_id or ensembl_gene_id
hgnc_file               a matrix for Converting gene symbol.
id_ava                  Gene id conversion types
id_conversion           Convert ENSEMBL gene id to gene Symbol in TCGA
id_conversion_vector    Gene id conversion
kegg_liver              a matrix of gene expression data in TCGA
module                  a matrix of module name, gene symbols, and the
                        number of gene symbols
prepare_chi             Preparer file for chi-square test
profile                 a matrix of gene expression data in TCGA
rep1                    Handle the case where one id corresponds to
                        multiple genes
rep2                    Handle the case where one id corresponds to
                        multiple genes
tcga_cli_deal           Combine clinical information obtained from TCGA
                        and extract survival data
ventricle               a matrix of gene expression data in GEO
