Man pages for huerqiang/GeoTcgaData
Processing Various Types of Data on GEO and TCGA
| 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... |
| 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... |
| fpkmToTpm | Convert fpkm to Tpm |
| gene_ave | Average the values of same genes in gene expression profile |
| gene_cov | a data.frame of gene length and GC content |
| geneExpress | a data.frame of gene expression data |
| 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... |
| 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 |
