# CGH Micro-Array NORmalization

## Documentation for package ‘MANOR’ version 1.14.0

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

amplicon.flag | Examples of flag objects to apply to CGH arrays
arrayTrend | Spatial trend of microarray spots statistic
chromosome.flag | Examples of flag objects to apply to CGH arrays
clone.qscore | Examples of qscore objects (quality scores) to apply to CGH arrays
control.flag | Examples of flag objects to apply to CGH arrays
dapi.snr.flag | Examples of flag objects to apply to CGH arrays
detectSB | Spatial bias detection
dyn.x.qscore | Examples of qscore objects (quality scores) to apply to CGH arrays
dyn.y.qscore | Examples of qscore objects (quality scores) to apply to CGH arrays
dynamics.qscore | Examples of qscore objects (quality scores) to apply to CGH arrays
edge | Examples of array-CGH data with spatial artifacts
flag | Create an object of type flag
flag.arrayCGH | Apply a flag to an arrayCGH
flag.summary | Summarize information about flags after array normalization
flags | Examples of flag objects to apply to CGH arrays
genome.plot | Pan-genomic representation of a normalized arrayCGH
global.spatial.flag | Examples of flag objects to apply to CGH arrays
gradient | Examples of array-CGH data with spatial artifacts
html.report | Generate an HTML report of array normalization
import | Import raw file to an arrayCGH object
import.default.aux | Import raw file to an arrayCGH object
import.gpr.aux | Import raw file to an arrayCGH object
import.spot.aux | Import raw file to an arrayCGH object
intensity.flag | Examples of flag objects to apply to CGH arrays
local.spatial.flag | Examples of flag objects to apply to CGH arrays
MANOR | Normalize an object of type arrayCGH
manor | Normalize an object of type arrayCGH
nem | Spatial Classification by EM algorithm
norm.arrayCGH | Normalize an object of type arrayCGH
pct.clone.qscore | Examples of qscore objects (quality scores) to apply to CGH arrays
pct.replicate.qscore | Examples of qscore objects (quality scores) to apply to CGH arrays
pct.spot.before.qscore | Examples of qscore objects (quality scores) to apply to CGH arrays
pct.spot.qscore | Examples of qscore objects (quality scores) to apply to CGH arrays
position.flag | Examples of flag objects to apply to CGH arrays
qscore | Create an object of type qscore
qscore.arrayCGH | arrayCGH quality score
qscore.summary | Compute quality scores for a given arrayCGH object
ref.snr.flag | Examples of flag objects to apply to CGH arrays
rep.flag | Examples of flag objects to apply to CGH arrays
replicate.flag | Examples of flag objects to apply to CGH arrays
report.plot | Array image and a genomic representation of a normalized arrayCGH
smoothness.qscore | Examples of qscore objects (quality scores) to apply to CGH arrays
SNR.flag | Examples of flag objects to apply to CGH arrays
sort.arrayCGH | Sort for normalized arrayCGH objects
spatial | Examples of array-CGH data with spatial artifacts
spatial.flag | Examples of flag objects to apply to CGH arrays
spot.flag | Examples of flag objects to apply to CGH arrays
to.flag | Create an object of type flag
to.qscore | Create an object of type qscore
unique.flag | Examples of flag objects to apply to CGH arrays
val.mark.flag | Examples of flag objects to apply to CGH arrays
var.replicate.qscore | Examples of qscore objects (quality scores) to apply to CGH arrays