Allele-specific Copy Number Analysis of whole genome data

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Documentation for package ‘patchwork’ version 2.4

Help Pages

alleledata patchwork alleledata function
applyref Apply reference to query data
assignAI A number of subfunctions used within patchwork.copynumbers().
check Karyotype check function
chromsCN Karyotype plotting for each chromosome post patchwork.copynumbers().
chrom_ucsc A number of subfunctions used within patchwork.copynumbers().
copynumbers Function plot allele-specific copy numbers of the genome
createreference Patchwork function to create your own normal reference file.
deChrom_ucsc A number of subfunctions used within patchwork.copynumbers().
GCNorm patchwork GC normalizing function
help.patchwork Welcome to patchwork
is.autosome A number of subfunctions used within patchwork.copynumbers().
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.copynumbers().
Medians_n_AI patchwork function which computes medians and allelec imbalance of the segment.
patchwork Patchwork main function
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.help Welcome to patchwork
patchwork.Medians_n_AI patchwork function which computes medians and allelec imbalance of the segment.
patchwork.plot Patchwork main function
patchwork.readChroms patchwork function to read chromosomes into R
patchwork.readme Welcome to patchwork
Patchwork.Region Detailed view of a selected regions of the genome.
patchwork.region Detailed view of a selected regions of the genome.
patchwork.segment patchwork segmentation function
patchwork.smoothing patchwork smoothing function
patchwork.subfunctions_copynumbers A number of subfunctions used within patchwork.copynumbers().
readChroms patchwork function to read chromosomes into R
readme.patchwork Welcome to patchwork
region Detailed view of a selected regions of the genome.
smoothing patchwork smoothing function
subfunctions_copynumbers A number of subfunctions used within patchwork.copynumbers().
weightedMean A number of subfunctions used within patchwork.copynumbers().
weightedMedian A number of subfunctions used within patchwork.copynumbers().