ap_norm2: Full AP data transformation
In cekehe/rappp: QC, data transformation and visualization for PAPP

View source: R/data_transformation_2_diff_input.R

ap_norm2

R Documentation

Full AP data transformation

Description

Wrapper function for full Autoimmunity Profiling data transformations.

Usage

ap_norm2(
  x,
  MADlimits = seq(0, 70, 5),
  na.rm = TRUE,
  check.names = FALSE,
  mad_center_prob = 0.5,
  mad_constant = 1,
  mad_low = FALSE,
  mad_high = FALSE,
  score_rightmost.closed = FALSE,
  score_left.open = FALSE,
  score_all.inside = FALSE,
  coselect_slope_cutoff = -0.5,
  coselect_offset = 0.1,
  coselect_bw = 0.1
)

Arguments

`x`	List with at least three elements, see Details for naming and content.
`MADlimits`	vector of MADs values used as boundaries for binning (≥MADs).
`na.rm`	logical, indicating whether NA values should be stripped before the computation proceeds. Altered default from `median()` and `mad()`.
`check.names`	logical, altered default from `data.frame()`.
`mad_center_prob`	value in [0,1] passed to prob in `quantile()`, defaults to the median.
`mad_constant`	constant for `mad()` function, default is 1 (compared to 1.4826 in base function).
`mad_low`	if TRUE, compute the ‘lo-median’, i.e., for even sample size, do not average the two middle values, but take the smaller one.(From `mad()`).
`mad_high`	if TRUE, compute the ‘hi-median’, i.e., take the larger of the two middle values for even sample size.(From `mad()`).
`score_rightmost.closed, score_left.open, score_all.inside`	logical, see `findInterval()` for details. Defaults result in scores for MADS ≥ cutoff, and any value below the lowest cutoff gets score 0.
`coselect_slope_cutoff`	Arbitrary slope cutoff value. Can be chosen freely.
`coselect_offset`	Offset used to prevent script from finding the peak (as slope = 0 there).
`coselect_bw`	Bandwidth for density funciton, default set to 0.1.

Details

Arguments starting with mad_ are specific for ap_mads2(), score_ for ap_scoring2(), and coselect_ for ap_cutoff_selection2(). These arguments are seldom altered.

The x list needs to include at least the elements:

MFI = assay mfi,

BEADS = Beads info (Filtered column with information about filtering),

SAMPLES = Sample info, if any should be excluded then these should be annotated in a column called "Filtered". Any samples with no text (ie. "") in such column will be included.