Processing Various Types of Data on GEO and TCGA

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Documentation for package ‘GeoTcgaData’ version 2.5.0

• 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