prepare.tcga.survival.data.old: Prepare FPKM data from TCGA project (specific tissue)

In averissimo/glmSparseNetPaper:

Description

This function will load data and pre-process it to be used in survival models.

Usage

prepare.tcga.survival.data.old(project = "brca",
  tissue.type = "primary.solid.tumor",
  handle.duplicates = "keep_first", coding.genes = FALSE,
  log2.pre.normalize = FALSE, normalization = "max")

Arguments

project	tcga project that has a package avaliable see https://github.com/averissimo/tcga.data
tissue.type	type of tissue, can be 'primary.solid.tumor', 'metastatic', etc... depending on project.

Details

It will: * load data * handle duplicate samples for same individal (default is to keep only first) * remove individuals with missing vital_status or both follow-up/death time span * remove individuals with follow-up/death time span == 0 * remove genes from RNASeqData (xdata) with standard deviation == 0

Value

a list with data ready to be used in survival analysis, the 'xdata.raw' and 'ydata.raw' elements have the full dataset for the specific tissue and the 'xdata' and 'ydata' have been cleaned by handling patients with multiple samples, removing individuals with event time <= 0, missing and genes that have standard_deviation == 0. It also returns a sha256 checksum for each of the data

Examples

prepare.tcga.survival.data('brca', 'primary.solid.tumor', 'keep_first')

averissimo/glmSparseNetPaper documentation built on Jan. 25, 2021, 12:11 p.m.