TCGAtumor_purity: Filters TCGA barcodes according to purity parameters

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

Description

TCGAtumor_purity Filters TCGA samples using 5 estimates from 5 methods as thresholds.

Usage

TCGAtumor_purity(barcodes, estimate, absolute, lump, ihc, cpe)

Arguments

barcodes	is a vector of TCGA barcodes
estimate	uses gene expression profiles of 141 immune genes and 141 stromal genes
absolute	which uses somatic copy-number data (estimations were available for only 11 cancer types)
lump	(leukocytes unmethylation for purity), which averages 44 non-methylated immune-specific CpG sites
ihc	as estimated by image analysis of haematoxylin and eosin stain slides produced by the Nationwide Childrens Hospital Biospecimen Core Resource
cpe	CPE is a derived consensus measurement as the median purity level after normalizing levels from all methods to give them equal means and s.ds

Value

List with $pure_barcodes attribute as a vector of pure samples and $filtered attribute as filtered samples with no purity info

Examples

dataTableSubt <- TCGAtumor_purity("TCGA-60-2721-01A-01R-0851-07",
                          estimate = 0.6,
                          absolute = 0.6,
                          ihc = 0.8,
                          lump = 0.8,
                          cpe = 0.7)

TCGAbiolinks documentation built on Nov. 8, 2020, 5:37 p.m.