getBetas: Get beta Values

In zwdzwd/sesame: SEnsible Step-wise Analysis of DNA MEthylation BeadChips

Get beta Values

Description

sum.typeI is used for rescuing beta values on Color-Channel-Switching CCS probes. The function takes a SigDF and returns beta value except that Type-I in-band signal and out-of-band signal are combined. This prevents color-channel switching due to SNPs.

Usage

getBetas(
  sdf,
  mask = TRUE,
  sum.TypeI = FALSE,
  collapseToPfx = FALSE,
  collapseMethod = c("mean", "minPval")
)

Arguments

sdf	SigDF
mask	whether to use mask
sum.TypeI	whether to sum type I channels
collapseToPfx	remove replicate to prefix (e.g., cg number) and remove the suffix
collapseMethod	mean or minPval

Value

a numeric vector, beta values

Examples

sesameDataCache() # if not done yet
sdf <- sesameDataGet('EPIC.1.SigDF')
betas <- getBetas(sdf)

zwdzwd/sesame documentation built on Dec. 21, 2024, 1:20 p.m.