preprocess.RawSignal

preprocess.RawSignal(
    meth,
    unmeth,
    probe_type,
    channel,
    oob_grn,
    oob_red,
    platform,
    sample_id,
    detection_p=None,
    steps=list(),
)

One sample’s in-band and out-of-band intensities, probe by probe.

The intermediate every step in the chain reads and writes. Keeping it explicit rather than passing a beta vector around is what lets detection be computed on the uncorrected out-of-band signal and background correction on the same numbers afterwards.

Methods

Name	Description
betas	M / (M + U + offset), with undetected probes set to NaN.

betas

preprocess.RawSignal.betas(offset=BETA_OFFSET, detection_p=DETECTION_P)

M / (M + U + offset), with undetected probes set to NaN.

NaN rather than a number, and this is the point of computing detection at all: a probe that did not rise above background has no measurement, and a beta of 0.43 from two noise readings is indistinguishable from a real 0.43 once it is in the matrix.