ap_ct: Coupling efficency test

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

Coupling efficency test

Description

Flags beads with signal similar to empty bead in coupling test, produces plot if wanted.

Usage

ap_ct(
  x,
  empty_bead,
  empty_co_multiple = 3,
  types = "PrEST",
  shouldplot = TRUE,
  shouldpdf = TRUE,
  filename = "coupling_efficiency.pdf",
  width = 25,
  height = 6,
  useDingbats = FALSE,
  ...
)

Arguments

x	List with at least three elements, see Deatils for naming and content.
empty_bead	Column index for empty bead.
empty_co_multiple	Number of sd above empty for cutoff.
types	Which types of beads should be included in flagging? See details.
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().
...	Further arguments passed to mean() and sd().

Details

The x list needs to include at least the elements CT = coupling test mfi,

BEADS = Beads info. See below for required columns.

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

The BEADS element needs at least the columns:

"Type" with info about type of content on bead, should include at least what is set in argument types (exact match). Eg. "PrEST" for PrESTs, or Full_length for full length representations,

"Plate" with numerical coupling plate number(s).

Note: The function plots to a layout containing two 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.