sb_corr {structToolbox}R Documentation

sbcms

Description

Signal/batch correction using SMCBMS package

Usage

sb_corr(
  order_col,
  batch_col,
  qc_col,
  smooth = 0,
  use_log = TRUE,
  min_qc = 4,
  qc_label = "QC",
  ...
)

Arguments

order_col

The sample-meta column containing the order of measurement.

batch_col

The sample_meta column containing the batch labels.

qc_col

The sample_meta column containing QC labels.

smooth

Spline smoothing parameter. Should be in the range 0 to 1. If set to 0 it will be estimated using leave-one-out cross-validation.

use_log

Perform the signal correction fit on the log scaled data. Default is TRUE.

min_qc

Minimum number of measured quality control (QC) samples required for signal correction within feature per batch. Default 4.

qc_label

The label used in qc_col to identify QC samples.

...

additional slots and values passed to struct_class

Value

struct object

Examples

M = sb_corr(order_col='run_order',batch_col='batch_no',qc_col='class')

[Package structToolbox version 1.0.1 Index]