# Processing Various Types of Data on GEO and TCGA

## Documentation for package ‘GeoTcgaData’ version 2.8.0

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

## Help Pages

array_preprocess | Preprocess of Microarray data
cal_mean_module | Find the mean value of the gene in each module
cluster_array | cluster probes of Microarray data
combine_pvalue | combine pvalues of SNP difference analysis result
countToFpkm | Convert count to FPKM
countToTpm | Convert count to Tpm
differential_array | Differential analysis of Microarray data
differential_CNV | Do difference analysis of gene level copy number variation data
differential_limma | differential_limma
differential_methy | differential_methy
differential_RNA | differential_RNA
differential_SNP | Do difference analysis of SNP data
differential_SNP_GEO | Do difference analysis of SNP data downloaded from GEO
differential_SNP_tcga | Do difference analysis of SNP data downloaded from TCGAbiolinks
fpkmToTpm | 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
get_geo_array | Get Microarray matrix data from GEO
GSE66705_sample2 | a matrix of gene expression data in GEO
id_conversion_TCGA | Convert ENSEMBL gene id to gene Symbol in TCGA
kegg_liver | a matrix of gene expression data in TCGA
Merge_methy_tcga | Merge methylation data downloaded from 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
repAssign | Handle the case where one id corresponds to multiple genes
repRemove | Handle the case where one id corresponds to multiple genes
SNP_QC | Do quality control of SNP data downloaded from TCGAbiolinks
ventricle | a matrix of gene expression data in GEO