patchwork: Allele-specific Copy Number Analysis of whole genome data
Version 2.4

Performs a allele-specific copy number analysis of whole genome data.

AuthorMarkus Mayrhofer, Sebastian DiLorenzo
Date of publication2017-02-03 12:39:12
MaintainerMarkus Mayrhofer <Markus.Mayrhofer@medsci.uu.se>
LicenseGPL-2
Version2.4
Package repositoryView on R-Forge
InstallationInstall the latest version of this package by entering the following in R:
install.packages("patchwork", repos="http://R-Forge.R-project.org")

Popular man pages

karyotype: karyotype plotting function
karyotype_chroms: Karyotype plotting of each chromosome
patchwork.alleledata: patchwork alleledata function
patchwork.applyref: Apply reference to query data
patchwork.copynumbers: Function plot allele-specific copy numbers of the genome
patchwork.GCNorm: patchwork GC normalizing function
patchwork.plot: Patchwork main function
See all...

All man pages Function index File listing

Man pages

karyotype: karyotype plotting function
karyotype_check: Karyotype check function
karyotype_chroms: Karyotype plotting of each chromosome
karyotype_chromsCN: Karyotype plotting for each chromosome post...
patchwork.alleledata: patchwork alleledata function
patchwork.applyref: Apply reference to query data
patchwork.copynumbers: Function plot allele-specific copy numbers of the genome
patchwork.createreference: Patchwork function to create your own normal reference file.
patchwork.GCNorm: patchwork GC normalizing function
patchwork.Medians_n_AI: patchwork function which computes medians and allelec...
patchwork.plot: Patchwork main function
patchwork.readChroms: patchwork function to read chromosomes into R
patchwork.region: Detailed view of a selected regions of the genome.
patchwork.segment: patchwork segmentation function
patchwork.smoothing: patchwork smoothing function
subfunctions_copynumbers: A number of subfunctions used within patchwork.copynumbers().
zzz: Welcome to patchwork

Functions

GCNorm Man page
Medians_n_AI Man page
Patchwork.Region Man page
alleledata Man page
applyref Man page
assignAI Man page Source code
check Man page
chrom_ucsc Man page Source code
chromsCN Man page
copynumbers Man page
createreference Man page
deChrom_ucsc Man page Source code
help.patchwork Man page
is.autosome Man page Source code
karyotype Man page Source code
karyotype_check Man page Source code
karyotype_chroms Man page Source code
karyotype_chromsCN Man page Source code
onLoad Source code
patchwork Man page
patchwork.GCNorm Man page Source code
patchwork.Medians_n_AI Man page Source code
patchwork.alleledata Man page Source code
patchwork.applyref Man page Source code
patchwork.copynumbers Man page Source code
patchwork.createreference Man page Source code
patchwork.help Man page
patchwork.plot Man page Source code
patchwork.readChroms Man page Source code
patchwork.readme Man page
patchwork.region Man page Source code
patchwork.segment Man page Source code
patchwork.smoothing Man page Source code
patchwork.subfunctions_copynumbers Man page
readChroms Man page
readme.patchwork Man page
region Man page
smoothing Man page
subfunctions_copynumbers Man page
weightedMean Man page Source code
weightedMedian Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/karyotype.r
R/karyotype_check.r
R/karyotype_chroms.r
R/karyotype_chromsCN.r
R/patchwork.GCNorm.r
R/patchwork.Medians_n_AI.r
R/patchwork.alleledata.r
R/patchwork.applyref.r
R/patchwork.copynumbers.r
R/patchwork.createreference.r
R/patchwork.plot.r
R/patchwork.readChroms.r
R/patchwork.region.r
R/patchwork.segment.r
R/patchwork.smoothing.r
R/subfunctions_copynumbers.r
R/sysdata.rda
R/zzz.R
inst
inst/README
inst/perl
inst/perl/mpile2alleles.pl
inst/perl/pile2alleles.pl
inst/python
inst/python/Pysamloader.py
man
man/karyotype.Rd
man/karyotype_check.Rd
man/karyotype_chroms.Rd
man/karyotype_chromsCN.Rd
man/patchwork.GCNorm.Rd
man/patchwork.Medians_n_AI.Rd
man/patchwork.alleledata.Rd
man/patchwork.applyref.Rd
man/patchwork.copynumbers.Rd
man/patchwork.createreference.Rd
man/patchwork.plot.Rd
man/patchwork.readChroms.Rd
man/patchwork.region.Rd
man/patchwork.segment.Rd
man/patchwork.smoothing.Rd
man/subfunctions_copynumbers.Rd
man/zzz.Rd
patchwork documentation built on May 21, 2017, 1:02 a.m.

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