Entry: MANOR-internal
Aliases: MANOR-internal add.lines arrayCGH2txt center check.names chrom cv flag.aggregate.arrayCGH my.aggregate.data.frame print.flag rename w num.chromosome.flag replicate.aux spot.corr.flag
Keywords: internal
Description: Internal Functions for MANOR Package
URL: ../../../library/MANOR/html/MANOR-internal.html

Entry: arrayTrend
Aliases: arrayTrend arrayTrend.default arrayTrend.arrayCGH
Keywords: 
Description: Spatial trend of microarray spots statistic
URL: ../../../library/MANOR/html/arrayTrend.html

Entry: detectSB
Aliases: detectSB detectSB.default detectSB.arrayCGH
Keywords: 
Description: Spatial bias detection
URL: ../../../library/MANOR/html/detectSB.html

Entry: flag
Aliases: to.flag flag
Keywords: 
Description: Create an object of type flag
URL: ../../../library/MANOR/html/flag.html

Entry: flag.arrayCGH
Aliases: flag.arrayCGH
Keywords: 
Description: Apply a flag to an arrayCGH
URL: ../../../library/MANOR/html/flag.arrayCGH.html

Entry: flag.summary
Aliases: flag.summary flag.summary.arrayCGH flag.summary.default
Keywords: 
Description: Summarize information about flags after array normalization
URL: ../../../library/MANOR/html/flag.summary.html

Entry: flags
Aliases: amplicon.flag chromosome.flag control.flag flags global.spatial.flag local.spatial.flag spatial.flag position.flag rep.flag replicate.flag SNR.flag ref.snr.flag dapi.snr.flag spot.flag unique.flag val.mark.flag
Keywords: datasets
Description: Examples of flag objects to apply to CGH arrays
URL: ../../../library/MANOR/html/flags.html

Entry: genome.plot
Aliases: genome.plot genome.plot.default genome.plot.arrayCGH
Keywords: 
Description: Display a pan-genomic representation of a normalized arrayCGH
URL: ../../../library/MANOR/html/genome.plot.html

Entry: html.report
Aliases: html.report html.report.arrayCGH html.report.default
Keywords: 
Description: Generate an HTML report of array normalization
URL: ../../../library/MANOR/html/html.report.html

Entry: import
Aliases: import import.default.aux import.gpr.aux import.spot.aux
Keywords: 
Description: Import raw file to an arrayCGH object
URL: ../../../library/MANOR/html/import.html

Entry: nem
Aliases: nem nem.default nem.arrayCGH
Keywords: 
Description: Spatial Classification by EM algorithm
URL: ../../../library/MANOR/html/nem.html

Entry: norm.arrayCGH
Aliases: norm.arrayCGH MANOR manor
Keywords: 
Description: Normalize an object of type arrayCGH
URL: ../../../library/MANOR/html/norm.arrayCGH.html

Entry: qscore
Aliases: to.qscore qscore
Keywords: 
Description: Create an object of type qscore
URL: ../../../library/MANOR/html/qscore.html

Entry: qscore.arrayCGH
Aliases: qscore.arrayCGH
Keywords: 
Description: Compute a quality score for a given arrayCGH
URL: ../../../library/MANOR/html/qscore.arrayCGH.html

Entry: qscore.summary
Aliases: qscore.summary.arrayCGH qscore.summary
Keywords: 
Description: Compute quality scores for a given arrayCGH object
URL: ../../../library/MANOR/html/qscore.summary.html

Entry: qscores
Aliases: clone.qscore pct.clone.qscore pct.spot.qscore pct.replicate.qscore smoothness.qscore dynamics.qscore var.replicate.qscore dyn.x.qscore dyn.y.qscore
Keywords: datasets
Description: Examples of qscore objects (quality scores) to apply to CGH arrays
URL: ../../../library/MANOR/html/qscores.html

Entry: report.plot
Aliases: report.plot report.plot.arrayCGH report.plot.default
Keywords: 
Description: Display an array image and a genomic representation of a normalized arrayCGH
URL: ../../../library/MANOR/html/report.plot.html

Entry: sort.arrayCGH
Aliases: sort.arrayCGH
Keywords: 
Description: sort clone-level information of a normalizaed arrayCGH object
URL: ../../../library/MANOR/html/sort.arrayCGH.html

Entry: spatial
Aliases: spatial edge edge.norm edge.txt gradient gradient.norm gradient.gpr
Keywords: datasets
Description: Examples of array-CGH data with spatial artifacts
URL: ../../../library/MANOR/html/spatial.html
