Last data update: 2014.03.03

Data Source

R Release (3.2.3)
CranContrib
BioConductor
All

Data Type

Packages
Functions
Images
Data set

Classification

Results 1 - 10 of 14 found.
[1] < 1 2 > [2]  Sort:

Formatting and output of Titan results (Package: TitanCNA) :

Function to format TitanCNA results in to a data.frame and output the results to a tab-delimited file.
● Data Source: BioConductor
● Keywords: IO, manip
● Alias: outputModelParameters, outputTitanResults
● 0 images

TitanCNA-package (Package: TitanCNA) :

TITAN is a software tool for inferring subclonal copy number alterations (CNA) and loss of heterozygosity (LOH). The algorithm also infers clonal group cluster membership for each event and the tumour proportion, or cellular prevalence, for each event.
● Data Source: BioConductor
● Keywords: IO, manip, package
● Alias: TitanCNA, TitanCNA-package
1 images

Plotting TITAN results (Package: TitanCNA) :

Three plotting functions for TitanCNA results. plotCNlogRByChr plots the copy number results from log ratio data. plotAllelicRatio plots the allelic imbalance and loss of heterozygosity (LOH) from allelic ratio data. plotClonalFrequency plots the clonal cluster and cellular prevalence results for each data point.
● Data Source: BioConductor
● Keywords: aplot, color
● Alias: plotAllelicRatio, plotCNlogRByChr, plotClonalFrequency, plotSubcloneProfiles
1 images

computeSDbwIndex (Package: TitanCNA) :

Compute the S_Dbw Validity Index internal cluster validation from the TitanCNA results to use for model selection.
● Data Source: BioConductor
● Keywords: manip
● Alias: computeSDbwIndex
● 0 images

correctReadDepth (Package: TitanCNA) :

Correct GC content and mappability biases in tumour sequence read counts using Loess curve fitting. Wrapper for function in HMMcopy.
● Data Source: BioConductor
● Keywords: IO, manip
● Alias: correctReadDepth
● 0 images

extractAlleleReadCounts (Package: TitanCNA) :

Function to extract allele read counts from a sequence alignment (BAM) file at specific positions of interest. The positions are passed in as the file path to a file in variant call format (VCF).
● Data Source: BioConductor
● Keywords: IO
● Alias: extractAlleleReadCounts
● 0 images

filterData (Package: TitanCNA) :

Filters all vectors in list based on specified chromosome(s) of interest, minimum and maximum read depths, missing data, mappability score threshold
● Data Source: BioConductor
● Keywords: manip
● Alias: filterData
● 0 images

getPositionOverlap (Package: TitanCNA) :

Given a list of chromosomes and positions, uses a C-based function that searches a list of segments to find the overlapping segment. Then, takes the value (4th column in segment data.frame) of the overlapping segment and assigns to the given chromosome and position.
● Data Source: BioConductor
● Keywords: manip
● Alias: getPositionOverlap
● 0 images

loadAlleleCounts (Package: TitanCNA) :

Function to load in the allele counts from tumour sequencing data from a delimited text file or data.frame object.
● Data Source: BioConductor
● Keywords: IO
● Alias: loadAlleleCounts
● 0 images

loadDefaultParameters (Package: TitanCNA) :

Load TITAN model parameters based on maximum copy number and number of clonal clusters.
● Data Source: BioConductor
● Keywords: attribute
● Alias: loadDefaultParameters
● 0 images