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

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

Author
Markus Mayrhofer, Sebastian DiLorenzo
Date of publication
2014-09-04 12:07:32
Maintainer
Markus Mayrhofer <Markus.Mayrhofer@medsci.uu.se>
License
GPL-2
Version
2.4

View on R-Forge

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

Files in this package

patchwork/DESCRIPTION
patchwork/NAMESPACE
patchwork/R
patchwork/R/karyotype.r
patchwork/R/karyotype_check.r
patchwork/R/karyotype_chroms.r
patchwork/R/karyotype_chromsCN.r
patchwork/R/patchwork.GCNorm.r
patchwork/R/patchwork.Medians_n_AI.r
patchwork/R/patchwork.alleledata.r
patchwork/R/patchwork.applyref.r
patchwork/R/patchwork.copynumbers.r
patchwork/R/patchwork.createreference.r
patchwork/R/patchwork.plot.r
patchwork/R/patchwork.readChroms.r
patchwork/R/patchwork.region.r
patchwork/R/patchwork.segment.r
patchwork/R/patchwork.smoothing.r
patchwork/R/subfunctions_copynumbers.r
patchwork/R/sysdata.rda
patchwork/R/zzz.R
patchwork/inst
patchwork/inst/README
patchwork/inst/perl
patchwork/inst/perl/mpile2alleles.pl
patchwork/inst/perl/pile2alleles.pl
patchwork/inst/python
patchwork/inst/python/Pysamloader.py
patchwork/man
patchwork/man/karyotype.Rd
patchwork/man/karyotype_check.Rd
patchwork/man/karyotype_chroms.Rd
patchwork/man/karyotype_chromsCN.Rd
patchwork/man/patchwork.GCNorm.Rd
patchwork/man/patchwork.Medians_n_AI.Rd
patchwork/man/patchwork.alleledata.Rd
patchwork/man/patchwork.applyref.Rd
patchwork/man/patchwork.copynumbers.Rd
patchwork/man/patchwork.createreference.Rd
patchwork/man/patchwork.plot.Rd
patchwork/man/patchwork.readChroms.Rd
patchwork/man/patchwork.region.Rd
patchwork/man/patchwork.segment.Rd
patchwork/man/patchwork.smoothing.Rd
patchwork/man/subfunctions_copynumbers.Rd
patchwork/man/zzz.Rd