# Processing various types of data on GEO and TCGA

## Documentation for package ‘GeoTcgaData’ version 1.0.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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
differential_cnv | Do chi-square test to find differential genes
diff_CNV | Do difference analysis of gene level copy number variation data
diff_gene | Get the differentially expressioned genes using DESeq2 package
diff_RNA | Do difference analysis of RNA-seq data
diff_SNP | Do difference analysis of SNP data
diff_SNP_tcga | Do difference analysis of SNP data downloaded from TCGAbiolinks
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
gene_cov | a data.frame of gene length and GC content
GSE66705_sample2 | a matrix of gene expression data in GEO
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
Merge_methy_tcga | Merge methylation data downloaded from TCGA
methyDiff | Get methylation difference gene
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