ba: ba.background

In metamaden/recountmethylation: Access and analyze public DNA methylation array data compilations

ba.background

Description

Get background signal for BeadArray metric calculations.

Get the Biotin staining Red BeadArray metric.

Get the Biotin staining Green BeadArray metric.

Get the Non-polymorphic Red BeadArray metric.

Get the Non-polymorphic Green BeadArray metric.

Get the Bisulfite Conversion I Red BeadArray metric.

Get the Restoration BeadArray metric.

Get the Specificity I Red BeadArray metric.

Get the Specificity I Green BeadArray metric.

Get the Specificity II Green BeadArray metric.

Get the Extension Red BeadArray metric.

Get the Extension Green BeadArray metric.

Get the Hybridication (high vs. medium) BeadArray metric.

Get the Hybridication (medium vs. low) BeadArray metric.

Get the Target Removal 1 BeadArray metric.

Get the Target Removal 2 BeadArray metric.

Get the Bisulfite Conversion I Green BeadArray metric.

Get the Bisulfite Conversion II BeadArray metric.

Usage

ba.background(cdf, ct = "Extension")

ba.biotinstaining.red(
  rs,
  biotin.baseline,
  rm,
  cdf,
  mnum = 1,
  mtot = 17,
  cnamei = "biotin.stain.red",
  ct = "Biotin|DNP"
)

ba.biotinstaining.grn(
  gs,
  biotin.baseline,
  rm,
  cdf,
  mnum = 2,
  mtot = 17,
  cnamei = "biotin.stain.grn",
  ct = "Biotin|DNP"
)

ba.nonpolymorphic.red(
  rs,
  rm,
  cdf,
  mnum = 3,
  mtot = 17,
  cnamei = "nonpolymorphic.red",
  ct = "NP"
)

ba.nonpolymorphic.grn(
  gs,
  rm,
  cdf,
  mnum = 4,
  mtot = 17,
  cnamei = "nonpolymorphic.grn",
  ct = "NP"
)

ba.bisulfiteconv1.red(
  rs,
  rm,
  cdf,
  mnum = 5,
  mtot = 17,
  cnamei = "bisulfite.conv1.red",
  ct = "Conversion I-"
)

ba.restoration(
  gs,
  rm,
  cdf,
  addr.bkg,
  baseline = 3000,
  mnum = 6,
  mtot = 17,
  cnamei = "restoration.grn",
  ct = "RESTORATION"
)

ba.specificity1.red(
  rs,
  rm,
  cdf,
  mnum = 7,
  mtot = 17,
  cnamei = "specificityI.red"
)

ba.specificity1.grn(
  gs,
  rm,
  cdf,
  mnum = 8,
  mtot = 17,
  cnamei = "specificityI.grn"
)

ba.specificity2(
  rs,
  gs,
  rm,
  cdf,
  mnum = 9,
  mtot = 17,
  cnamei = "specificityII",
  ct = "Specificity 2"
)

ba.extension.red(
  rs,
  rm,
  cdf,
  mnum = 10,
  mtot = 17,
  cnamei = "extension.red",
  ct = "Extension.*"
)

ba.extension.grn(
  gs,
  rm,
  cdf,
  mnum = 11,
  mtot = 17,
  cnamei = "extension.grn",
  ct = "Extension.*"
)

ba.hybridization.hi.vs.med(
  gs,
  rm,
  cdf,
  mnum = 12,
  mtot = 17,
  cnamei = "hyb.hi.med",
  ct = "High|Medium"
)

ba.hybridization.med.vs.low(
  gs,
  rm,
  cdf,
  mnum = 13,
  mtot = 17,
  cnamei = "hyb.med.low",
  ct = "Low|Medium"
)

ba.targetremoval1(
  gs,
  rm,
  cdf,
  baseline = 3000,
  mnum = 14,
  mtot = 17,
  cnamei = "target.removal1",
  ct = "Extension|Target Removal 1"
)

ba.targetremoval2(
  gs,
  rm,
  cdf,
  baseline = 3000,
  mnum = 15,
  mtot = 17,
  cnamei = "target.removal2",
  ct = "Extension|Target Removal 2"
)

ba.bisulfiteconv1.grn(
  gs,
  rm,
  cdf,
  mnum = 16,
  mtot = 17,
  cnamei = "bisulfite.conv1.grn",
  ct = "Conversion I-"
)

ba.bisulfiteconv2(
  rs,
  gs,
  rm,
  cdf,
  mnum = 17,
  mtot = 17,
  cnamei = "bisulfite.conv2",
  ct = "Conversion II-"
)

Arguments

cdf	Control probe data frame (required).
ct	Column name/metric title (character, required).
rs	Red signal matrix (required).
biotin.baseline	Baseline signal for the biotin stain assay (required).
rm	Results matrix containing control metrics (required).
mnum	Metric number out of total (numeric).
mtot	Total metrics to be calculated (numeric, 17).
cnamei	Column name (character, required).
gs	Green signal matrix (required).
addr.bkg	Background signal probe address (required).
baseline	Baseline measure for signals (integer, 3000).

metamaden/recountmethylation documentation built on Jan. 5, 2023, 9:56 a.m.