get_qcsignal {recountmethylation} | R Documentation

## 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)

[Package recountmethylation version 1.4.5 Index]