get_betas: Get Methylation Beta Values

In fynnwi/intratumormeth: Intratumor DNA Methylation Analysis

Get Methylation Beta Values

Description

Loads the previously generated methylation beta values from disk and retuns them in a matrix. This function allows to specify probe and sample filters. These should be specified as character vectors containing probe/sample ids. Furthermore, the normalization method can be specified. Probes that contain NA values can be removed from all samples by specifying removeNaProbes = TRUE.

Usage

get_betas(
  outputDir,
  probeFilter = NULL,
  sampleFilter = NULL,
  normalization = "raw",
  removeNaProbes = FALSE
)

Arguments

outputDir	Output directory of the intratumormeth study.
probeFilter	Character vector containing probe ids that should be filtered out.
sampleFilter	Character vector containing sample ids that should be filtered out.
normalization	Should be either "raw", "noob", or "swan".
removeNaProbes	If TRUE, beta values of probes that are NA for at least one sample will be removed.

Value

Matrix containing methylation beta values with CpG probes as rows and sample ids as columns.

fynnwi/intratumormeth documentation built on March 29, 2022, 12:06 a.m.