parseGEOsignalMU: Convert signal M and U to SigDF

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

Convert signal M and U to SigDF

Description

This overcomes the issue of missing IDAT files. However, out-of-band signals will be missing or faked (sampled from a normal distribution).

Usage

parseGEOsignalMU(
  sigM,
  sigU,
  Probe_IDs,
  oob.mean = 500,
  oob.sd = 300,
  platform = NULL
)

Arguments

sigM	methylated signal, a numeric vector
sigU	unmethylated signal, a numirc vector
Probe_IDs	probe ID vector
oob.mean	assumed mean for out-of-band signals
oob.sd	assumed standard deviation for out-of-band signals
platform	platform code, will infer if not given

Value

SigDF

Examples

sigM <- c(11436, 6068, 2864)
sigU <- c(1476, 804, 393)
probes <- c("cg07881041", "cg23229610", "cg03513874")
sdf <- parseGEOsignalMU(sigM, sigU, probes, platform = "EPIC")

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