QCtablePlot: Compute and plot a table of QC statistics

In ammar257ammar/ArrayAnalysis-Bioconductor: ArrayAnalysis

Compute and plot a table of QC statistics

Description

This function (from functions_imagesQC.R) computes and plots a table of QC statistics based on the qc (simpleaffy Bioconductor package) and yaqc (yaqcaffy Bioconductor package) functions, which generally only work for chiptypes with perfect match and mismatch probes, but even not for all of those. As such, when these statistics are not provided as parameters, trys are used in this function to compute them internally. Values for which the try fails are not computed, but the script will continue after giving a warning.

Usage

QCtablePlot(
  Data,
  quality = NULL,
  sprep = NULL,
  lys = NULL,
  samplePrep = TRUE,
  ratio = TRUE,
  hybrid = TRUE,
  percPres = TRUE,
  bgPlot = TRUE,
  scaleFact = TRUE,
  WIDTH = 1000,
  HEIGHT = 1414,
  POINTSIZE = 24
)

Arguments

Data	(Status: required) The raw data object (datatype: AffyBatch)
quality	(Status: optional, Default:NULL) object obtained by calling the qc function (simpleaffy).When not provided, it is computed within the function.(datatype: QCStats)
sprep	(Status: optional, Default:NULL) A matrix of 3’probe intensities for dap, thr, lys, and phe, taken from an object of class YAQCStats (yaqc function, yaqcaffy). When not provided, it is computed within the function. (datatype: matrix)
lys	(Status: optional, Default:NULL) Matrix of A, M, P calls for the 3’ probeset of Lys on each array, based on results from the detection.p.val function (simpleaffy) . When not provided, it is computed within the function. (datatype: matrix)
samplePrep	(Status: optional, Default:TRUE) Does the table have to contain sample preparation QC statistics? (datatype: logical)
ratio	(Status: optional, Default:TRUE) Does the table have to contain 3’/5’ ratio statistics? (datatype: logical)
hybrid	(Status: optional, Default:TRUE) Does the table have to contain hybridisation QC statistics? (datatype: logical)
percPres	(Status: optional, Default:TRUE) Does the table have to contain percentage present QC statistics? (datatype: logical)
bgPlot	(Status: optional, Default:TRUE) Does the table have to contain background signal intensity QC statistics? (datatype: logical)
scaleFact	(Status: optional, Default:TRUE) Does the table have to contain scale factor QC statistics?(datatype: logical)
WIDTH	(Status: optional, Default:1000) png image width (datatype: number)
HEIGHT	(Status: optional, Default:1414) png image height (datatype: number)
POINTSIZE	(Status: optional, Default:24) png image point size (datatype: number)

Value

A PNG file called ‘QCtable’ with the requested statistics

Examples

# By default, the script will call:
# computeQCtable(rawData, quality, sprep, lys, samplePrep = samplePrep,
# ratio = ratio, hybrid = hybrid, percPres = percPres, bgPlot = bgPlot, scaleFact = scaleFact)

ammar257ammar/ArrayAnalysis-Bioconductor documentation built on Jan. 29, 2024, 7:21 a.m.