TCGAtumor_purity: Filters TCGA barcodes according to purity parameters

Description Usage Arguments Value Examples

Description

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

Usage

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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

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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.