getClinic: getClinic to download clinic data for certain cancer types...
In ELMER: Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes

Description Usage Arguments Value

View source: R/FetchTCGA.R

getClinic is a function to download latest version of clinic data for all samples of certain cancer types from TCGA website.

1	getClinic(disease, basedir = "./Data")

`disease`	A character specifies the disease to download from TCGA such as BLCA
`basedir`	A path shows where the data will be stored.

Download all clinic information for the specified disease.

ELMER documentation built on Nov. 8, 2020, 4:59 p.m.

ELMER index

11 - ELMER: Use case 2 - Introduction: Input data 3.1 - Data input - Creating MAE object 3.2 - Identifying differentially methylated probes 3.3 - Identifying putative probe-gene pairs 3.4 - Motif enrichment analysis on the selected probes 3.5 - Identifying regulatory TFs 3.6 - TCGA.pipe: Running ELMER for TCGA data in a compact way 4.1 - Scatter plots 4.2 - Schematic plots 4.3 - Motif enrichment plots 4.4 - Regulatory TF plots 4.5 - Heatmap plots 5 - Integrative analysis workshop with TCGAbiolinks and ELMER - Analysis GUI ELMER v.2: An R/Bioconductor package to reconstruct gene regulatory networks from DNA methylation and transcriptome profiles

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