Man pages for GeoTcgaData
Processing various types of data on GEO and TCGA
| arrayDiff | arrayDiff |
| cal_mean_module | Find the mean value of the gene in each module |
| classify_sample | Get the differentially expressioned genes using DESeq2... |
| countToFpkm_matrix | Convert count to FPKM |
| countToTpm_matrix | Convert count to Tpm |
| diff_CNV | Do difference analysis of gene level copy number variation... |
| differential_cnv | Do chi-square test to find differential genes |
| diff_gene | Get the differentially expressioned genes using DESeq2... |
| Diff_limma | Diff_limma |
| diff_RNA | Do difference analysis of RNA-seq data |
| diff_RNA_ucsc | Do difference analysis of RNA-seq data downloaded from ucsc |
| diff_SNP | Do difference analysis of SNP data |
| diff_SNP_tcga | Do difference analysis of SNP data downloaded from... |
| fpkmToTpm_matrix | 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 |
| 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 |
| methyDiff_ucsc | Title |
| 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 |
| 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... |
| ventricle | a matrix of gene expression data in GEO |
