ap_igx: Loading control

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

Loading control

Description

Filter samples with low MFI for the anti-human IgX bead.

Usage

ap_igx(
  x,
  IgX_bead,
  IgType = "G",
  species = "h",
  IgX_cutoff = 5000,
  cosfac = c(3, -3),
  internal_sampID = "sample_name",
  external_sampID = "tube_label",
  shouldplot = TRUE,
  shouldpdf = TRUE,
  filename = "anti-humanIgX.pdf",
  width = 12,
  height = 6,
  useDingbats = FALSE,
  ...
)

Arguments

x	List with at least three elements, see Deatils for naming and content.
IgX_bead	Column index for anti-IgX bead.
IgType	Which Imunoglobulin is measured, default is G.
species	letter for which species is measured, affects text in output.
IgX_cutoff	MFI cutoff value for filtering.
cosfac	Median absolute deviation multipliers in vector c(upper, lower), for drawing lines and detecting potential outliers.
internal_sampID	Column name in SAMPLES with internal sample IDs, such as from LIMS. Replicates (named with one of pool|rep|mix|commercial, not case sensitive) and blanks (named with one of empty|blank|buffer, not case sensitive) must be stated in this column.
external_sampID	Column name in SAMPLES with externaö sample IDs, such as given from the collaborator or user.
shouldplot	Logical, should a plot be made?
shouldpdf	Logical, should it plot to pdf?
filename	String with filename and desired path, end with .pdf
width, height	Width and height for pdf, see pdf().
useDingbats	Logical. Default is FALSE, compared to in default pdf().
...	Arguments are passed to base plot function.

Details

The x list needs to include at least the elements:

MFI = assay mfi,

SAMPLES = Sample info. See below for required columns.

FILTERINFO = Vector with info on which filter steps has been done.

The SAMPLES element needs at least the columns:

"AssayWell" with Well IDs in the assay plate, e.g A01, B01 etc.,

Note: The function plots to a layout containing seven areas.

Value

Updated input x with relevant filtering info and a pdf with plot (if shouldplot=TRUE and shouldpdf=TRUE).

cekehe/rappp documentation built on May 17, 2022, 8:54 a.m.