get_qcsignal: get_qcsignal

In metamaden/recountmethylation: Access and analyze public DNA methylation array data compilations

get_qcsignal

Description

Get the medians of the log2-transformed M and U signals. This function uses the DelayedMatrixStats implementations of colMedians for rapid calculations on DelayedArray-formatted matrices.

Usage

get_qcsignal(se = NULL, mm = NULL, mu = NULL, sample_idv = NULL)

Arguments

se	Valid SummarizedExperiment object, such as a MethylSet or similar object for which getMeth() and getUnmeth() methods are defined (optional).
mm	Matrix of methylated/M signals (optional, not required if se provided).
mu	Matrix of unmethylated/U signals (optional, not required if se provided).
sample_idv	Vector of sample IDs to label rows in the returned data frame (optional, uses mm colnames instead if not provided).

Details

Calculates the log2 of median signal for methylated/M and unmethylated/U signals separately.

Value

Data frame of signal summaries.

See Also

bactrl

Examples

library(minfiData)
data(MsetEx)
se <- MsetEx
class(se)
# [1] "MethylSet"
# attr(,"package")
# [1] "minfi"
ms <- get_qcsignal(se)

metamaden/recountmethylation documentation built on Jan. 5, 2023, 9:56 a.m.