dot-get_TCGA_CNV_ratio: Read CNV ratio dataset from TCGA

In a3609640/eIF4F.analysis: A R package to analyze eIF4F subunits in human cancers

Read CNV ratio dataset from TCGA

Description

This function reads the CNV ratio data broad.mit.edu_PANCAN_Genome_Wide_SNP_6_whitelisted.gene.xena, in which CNV ratios were calculated by dividing, for each gene, the estimated gene-level CNV values in malignant tumors to the average CNV value in normal adjacent tissues (NATs) of the same cancer type.

Usage

.get_TCGA_CNV_ratio()

Details

The function also removes possible duplicated tumor samples and samples with NAs in the dataset.

It should not be used directly, only inside initialize_cnv_data() function.

Value

a data frame that contains CNV ratio data for each tumor

See Also

Other helper function for data initialization: .get_TCGA_CNV_value(), .get_TCGA_CNV(), .get_TCGA_GTEX_RNAseq(), .get_TCGA_RNAseq()

Examples

## Not run: 
.get_TCGA_CNV_ratio()

## End(Not run)

a3609640/eIF4F.analysis documentation built on Jan. 2, 2023, 11:19 p.m.