TCGAtumor_purity {TCGAbiolinks} | R Documentation

## Filters TCGA barcodes according to purity parameters

### 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

    pam50 <- TCGAtumor_purity("TCGA-60-2721-01A-01R-0851-07",
                              estimate = 0.6,
                              absolute = 0.6,
                              ihc = 0.8,
                              lump = 0.8,
                              cpe = 0.7)

[Package TCGAbiolinks version 2.8.4 Index]