R Graphical Manual

Last data update: 2014.03.03

Data Source

R Release (3.2.3)
CranContrib
BioConductor
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Classification

Results 1 - 10 of 10 found.
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runHMM (Package: CNOGpro) :

Implements a Viterbi algorithm for assigning most likely copy number to each chromosomal position in the chromosome.

● Data Source: CranContrib
● Keywords:
● Alias: runHMM
● 3 images

plotCNOGpro (Package: CNOGpro) :

Plots the coverage in a number of ways: Coverage along the chromosome, density plots of coverage for each individual copy number state (as assigned by the runHMMmethod) and coverage by GC percentage of the reads, before and after normalization.

● Data Source: CranContrib
● Keywords:
● Alias: plotCNOGpro
● 3 images

normalizeGC (Package: CNOGpro) :

Manipulates count values from windows of comparatively high or low GC content so as to bring the counts more in line with those from median GC-content windows.

● Data Source: CranContrib
● Keywords:
● Alias: normalizeGC
● 2 images

store (Package: CNOGpro) :

Prints the relevant data to a text file. By default, the entire gene table including copy numbers inferred by bootstrapping and HMM is printed. However, using the flag outputEntireTable=F will make the function print only the HMM breakpoints with associated most probable states.

● Data Source: CranContrib
● Keywords:
● Alias: store
● 0 images

printCNOGpro (Package: CNOGpro) :

Results are printed to stout. The default behavior is to print the HMMtable. If this does not exist, the function will attempt to print the gene table (with copy numbers.)

● Data Source: CranContrib
● Keywords:
● Alias: printCNOGpro
● 0 images

summaryCNOGpro (Package: CNOGpro) :

Prints basic parameters of the experiment.

● Data Source: CranContrib
● Keywords:
● Alias: summaryCNOGpro
● 0 images

CNOGpro-package (Package: CNOGpro) :

Detects copy number variation in resequencing experiments

● Data Source: CranContrib
● Keywords: package
● Alias: CNOGpro-package
● 0 images

runBootstrap (Package: CNOGpro) :

For each genetic element in the gene table of a CNOGpro object, sample repeatedly from the read observations associated with that gene while replacing the observations.

● Data Source: CranContrib
● Keywords:
● Alias: runBootstrap
● 0 images

CNOGpro (Package: CNOGpro) : Set up a new CNOGpro experiment

This function initializes the CNOGpro experiment.

● Data Source: CranContrib
● Keywords:
● Alias: CNOGpro
● 2 images

CNOGpro-internal (Package: CNOGpro) : Internal CNOGpro Functions

Internal CNOGpro functions

● Data Source: CranContrib
● Keywords: internal
● Alias: HMMcopynumber, addState, calculateProb, copynumberBootstrap, getGCinwindows, getMembership, gethits, getreadcounts, getsequence, insertRow, isbetween, makeViterbimat, readGenBank, rgammapois, sampleChromosome, setupEmissionMatrix, setupTransitionMatrix, solvePR, spans, updateGeneTable
● 0 images