Tumor.purity: TCGA samples with their Tumor Purity measures
In BioinformaticsFMRP/TCGAbiolinks: TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data
Tumor.purity R Documentation
TCGA samples with their Tumor Purity measures
Description
A dataset containing the Sample Ids from TCGA tumor purity measured according to 4 estimates attributes of 9364 tumor patients
Usage
Tumor.purity
Format
A data frame with 9364 rows and 7 variables:
- Sample.ID
Sample ID from TCGA barcodes, character string
- Cancer.type
Cancer type, character string
- ESTIMATE
uses gene expression profiles of 141 immune genes and 141 stromal genes, 0-1 value
- ABSOLUTE
uses somatic copy-number data (estimations were available for only 11 cancer types), 0-1 value
- LUMP
(leukocytes unmethylation for purity), which averages 44 non-methylated immune-specific CpG sites,
0-1value
- IHC
as estimated by image analysis of haematoxylin and eosin stain slides produced by the Nationwide
Childrens Hospital Biospecimen Core Resource, 0-1 value
- CPE
derived consensus measurement as the median purity level after normalizing levels from all methods to
give them equal means and s.ds, 0-1 value
...
Source
BioinformaticsFMRP/TCGAbiolinks documentation built on April 12, 2024, 2:08 a.m.
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| Tumor.purity | R Documentation |
TCGA samples with their Tumor Purity measures
Description
A dataset containing the Sample Ids from TCGA tumor purity measured according to 4 estimates attributes of 9364 tumor patients
Usage
Tumor.purity
Format
A data frame with 9364 rows and 7 variables:
- Sample.ID
Sample ID from TCGA barcodes, character string
- Cancer.type
Cancer type, character string
- ESTIMATE
uses gene expression profiles of 141 immune genes and 141 stromal genes, 0-1 value
- ABSOLUTE
uses somatic copy-number data (estimations were available for only 11 cancer types), 0-1 value
- LUMP
(leukocytes unmethylation for purity), which averages 44 non-methylated immune-specific CpG sites, 0-1value
- IHC
as estimated by image analysis of haematoxylin and eosin stain slides produced by the Nationwide Childrens Hospital Biospecimen Core Resource, 0-1 value
- CPE
derived consensus measurement as the median purity level after normalizing levels from all methods to give them equal means and s.ds, 0-1 value
...
Source
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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