TCGAanalyze_copynumber

data

threshold


Identifying Segment Gain Or Loss (SGOL) using findMCR package
Example:
query &lt;- TCGAquery("acc","genome_wide_snp_6", level = 3)
TCGAdownload(query,"trash")
data &lt;- TCGAprepare(query,"trash",  type = "nocnv_hg19")


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.

Antonio Colaprico

TCGAbiolinks

TCGAbiolinks: An R/Bioconductor package for integrative analysis with
TCGA data

TCGAanalyze_copynumber function


Identifying Segment Gain Or Loss (SGOL) using findMCR package
Example:
query <- TCGAquery("acc","genome_wide_snp_6", level = 3)
TCGAdownload(query,"trash")
data <- TCGAprepare(query,"trash",  type = "nocnv_hg19")


TCGAanalyze_copynumber: Identifying Segment Gain Or Loss (SGOL)

Description

Usage

Arguments

Value

Examples