MANOR: CGH Micro-Array NORmalization

Importation, normalization, visualization, and quality control functions to correct identified sources of variability in array-CGH experiments.

Author
Pierre Neuvial <pierre.neuvial@genopole.cnrs.fr>, Philippe Hupe <philippe.hupe@curie.fr>
Date of publication
None
Maintainer
Pierre Neuvial <pierre.neuvial@genopole.cnrs.fr>
License
GPL-2
Version
1.46.0
URLs

View on Bioconductor

Man pages

arrayTrend
Spatial trend of microarray spots statistic
detectSB
Spatial bias detection
flag.arrayCGH
Apply a flag to an arrayCGH
flags
Examples of flag objects to apply to CGH arrays
flag.summary
Summarize information about flags after array normalization
genome.plot
Pan-genomic representation of a normalized arrayCGH
html.report
Generate an HTML report of array normalization
import
Import raw file to an arrayCGH object
MANOR-internal
Internal Functions for MANOR Package
nem
Spatial Classification by EM algorithm
norm
Normalize an object of type arrayCGH
qscore
Create an object of type qscore
qscore.arrayCGH
arrayCGH quality score
qscores
Examples of qscore objects (quality scores) to apply to CGH...
qscore.summary
Compute quality scores for a given arrayCGH object
report.plot
Array image and a genomic representation of a normalized...
sort
Sorting for normalized arrayCGH objects
spatial
Examples of array-CGH data with spatial artifacts
to.flag
Create an object of type flag

Files in this package

MANOR/DESCRIPTION
MANOR/NAMESPACE
MANOR/R
MANOR/R/arrayCGH2txt.R
MANOR/R/arrayTrend.R
MANOR/R/detectSB.R
MANOR/R/flag.arrayCGH.R
MANOR/R/flag.summary.R
MANOR/R/genome.plot.R
MANOR/R/html.report.R
MANOR/R/import.R
MANOR/R/intensity.plot.R
MANOR/R/nem.R
MANOR/R/norm.R
MANOR/R/quality.R
MANOR/R/report.plot.R
MANOR/R/sort.R
MANOR/R/to.flag.R
MANOR/R/utils.R
MANOR/build
MANOR/build/vignette.rds
MANOR/data
MANOR/data/flags.RData
MANOR/data/qscores.RData
MANOR/data/spatial.RData
MANOR/inst
MANOR/inst/NEWS
MANOR/inst/doc
MANOR/inst/doc/MANOR.R
MANOR/inst/doc/MANOR.Rnw
MANOR/inst/doc/MANOR.pdf
MANOR/inst/extdata
MANOR/inst/extdata/edge.txt
MANOR/inst/extdata/gradient.gpr
MANOR/inst/system
MANOR/inst/system/checkDataObjects.R
MANOR/man
MANOR/man/MANOR-internal.Rd
MANOR/man/arrayTrend.Rd
MANOR/man/detectSB.Rd
MANOR/man/flag.arrayCGH.Rd
MANOR/man/flag.summary.Rd
MANOR/man/flags.Rd
MANOR/man/genome.plot.Rd
MANOR/man/html.report.Rd
MANOR/man/import.Rd
MANOR/man/nem.Rd
MANOR/man/norm.Rd
MANOR/man/qscore.Rd
MANOR/man/qscore.arrayCGH.Rd
MANOR/man/qscore.summary.Rd
MANOR/man/qscores.Rd
MANOR/man/report.plot.Rd
MANOR/man/sort.Rd
MANOR/man/spatial.Rd
MANOR/man/to.flag.Rd
MANOR/src
MANOR/src/Rnem_arg.c
MANOR/src/Rnem_exe.c
MANOR/src/exememo.c
MANOR/src/genmemo.h
MANOR/src/nem_alg.c
MANOR/src/nem_alg.h
MANOR/src/nem_arg.h
MANOR/src/nem_hlp.c
MANOR/src/nem_hlp.h
MANOR/src/nem_mod.c
MANOR/src/nem_mod.h
MANOR/src/nem_nei.c
MANOR/src/nem_nei.h
MANOR/src/nem_rnd.c
MANOR/src/nem_rnd.h
MANOR/src/nem_typ.h
MANOR/src/nem_ver.c
MANOR/src/nem_ver.h
MANOR/vignettes
MANOR/vignettes/MANOR.Rnw
MANOR/vignettes/MANOR.bib
MANOR/vignettes/html.sty
MANOR/vignettes/index.html
MANOR/vignettes/natbib.sty