dot-get_TCGA_CNV: Read CNV threshold dataset from TCGA

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

Read CNV threshold dataset from TCGA

Description

This function reads the threshold CNV data Gistic2_CopyNumber_Gistic2_all_thresholded.by_genes, which grouped the CNV values with thresholds 3+, 3, 2, 1, 0, to represent high-level copy number gain, low-level copy number gain, diploid, shallow deletion, or deep deletion.

Usage

.get_TCGA_CNV()

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 threshold data for all TCGA tumor

See Also

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

Examples

## Not run: 
.get_TCGA_CNV()

## End(Not run)

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