TCGAbiolinks包帮助文档（英文版）

colDataPrepare

Create samples information matrix for GDC samples

gaiaCNVplot

Creates a plot for GAIA ouptut (all significant aberrant regions.)

GDCdownload

Download GDC data

GDCprepare

Prepare GDC data

GDCprepare_clinic

Parsing clinical xml files

GDCquery

Query GDC data

GDCquery_ATAC_seq

Retrieve open access ATAC-seq files from GDC server

GDCquery_clinic

Get GDC clinical data

GDCquery_Maf

Retrieve open access maf files from GDC server

get.GRCh.bioMart

Get hg19 or hg38 information from biomaRt

getAdjacencyBiogrid

Get a matrix of interactions of genes from biogrid

getDataCategorySummary

Create a Summary table for each sample in a project saying if it contains or not files for a certain data category

getGDCInfo

Check GDC server status

getGDCprojects

Retrieve all GDC projects

getGistic

Download GISTIC data from firehose

getManifest

Get a Manifest from GDCquery output that can be used with GDC-client

getResults

Get the results table from query

getSampleFilesSummary

Retrieve summary of files per sample in a project

getTSS

getTSS to fetch GENCODE gene annotation (transcripts level) from Bioconductor package biomaRt If upstream and downstream are specified in TSS list, promoter regions of GENCODE gene will be generated.

get_IDs

Extract information from TCGA barcodes.

isServeOK

Check GDC server status is OK

matchedMetExp

Get GDC samples with both DNA methylation (HM450K) and Gene expression data from GDC databse

PanCancerAtlas_subtypes

Retrieve table with TCGA molecular subtypes

TabSubtypesCol_merged

TCGA samples with their Pam50 subtypes

TCGAanalyze_analyseGRN

Generate network

TCGAanalyze_Clustering

Hierarchical cluster analysis

TCGAanalyze_DEA

Differential expression analysis (DEA) using edgeR or limma package.

TCGAanalyze_DEA_Affy

Differentially expression analysis (DEA) using limma package.

TCGAanalyze_DMR

Differentially methylated regions Analysis

TCGAanalyze_EA

Enrichment analysis of a gene-set with GO [BP,MF,CC] and pathways.

TCGAanalyze_EAcomplete

Enrichment analysis for Gene Ontology (GO) [BP,MF,CC] and Pathways

TCGAanalyze_Filtering

Filtering mRNA transcripts and miRNA selecting a threshold.

TCGAanalyze_LevelTab

Adding information related to DEGs genes from DEA as mean values in two conditions.

TCGAanalyze_networkInference

infer gene regulatory networks

TCGAanalyze_Normalization

normalization mRNA transcripts and miRNA using EDASeq package.

TCGAanalyze_Pathview

Generate pathview graph

TCGAanalyze_Preprocessing

Array Array Intensity correlation (AAIC) and correlation boxplot to define outlier

TCGAanalyze_survival

Creates survival analysis

TCGAanalyze_SurvivalKM

survival analysis (SA) univariate with Kaplan-Meier (KM) method.

TCGAbatch_Correction

Batch correction using ComBat and Voom transformation using limma package.

TCGAbiolinks

The aim of TCGAbiolinks is : i) facilitate the TCGA open-access data retrieval, ii) prepare the data using the appropriate pre-processing strategies, iii) provide the means to carry out different standard analyses and iv) allow the user to download a specific version of the data and thus to easily reproduce earlier research results. In more detail, the package provides multiple methods for analysis (e.g., differential expression analysis, identifying differentially methylated regions) and methods for visualization (e.g., survival plots, volcano plots, starburst plots) in order to easily develop complete analysis pipelines.

TCGAprepare_Affy

Prepare CEL files into an AffyBatch.

TCGAquery_MatchedCoupledSampleTypes

Retrieve multiple tissue types from the same patients.

TCGAquery_recount2

Query gene counts of TCGA and GTEx data from the Recount2 project

TCGAquery_SampleTypes

Retrieve multiple tissue types not from the same patients.

TCGAquery_subtype

Retrieve molecular subtypes for a given tumor

TCGAtumor_purity

Filters TCGA barcodes according to purity parameters

TCGAvisualize_BarPlot

Barplot of subtypes and clinical info in groups of gene expression clustered.

TCGAvisualize_EAbarplot

barPlot for a complete Enrichment Analysis

TCGAvisualize_Heatmap

Heatmap with more sensible behavior using heatmap.plus

TCGAvisualize_meanMethylation

Mean methylation boxplot

TCGAvisualize_oncoprint

Creating a oncoprint

TCGAvisualize_PCA

Principal components analysis (PCA) plot

TCGAvisualize_starburst

Create starburst plot

TCGAvisualize_SurvivalCoxNET

Survival analysis with univariate Cox regression package (dnet)

TCGAVisualize_volcano

Creates a volcano plot for DNA methylation or expression

TCGA_MolecularSubtype

Retrieve molecular subtypes for given TCGA barcodes

Tumor.purity

TCGA samples with their Tumor Purity measures

UseRaw_afterFilter

Use raw count from the DataPrep object which genes are removed by normalization and filtering steps.