probability
(Package: VanillaICE) :
Accessor for probability filter
Accessor for probability filter
● Data Source:
BioConductor
● Keywords:
● Alias: probability
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read.bsfiles
(Package: VanillaICE) :
Deprecated function in VanillaICE
The function read.bsfiles has been deprecated. This function is provided only for compatability with older versions and will be defunct at the next release.
● Data Source:
BioConductor
● Keywords: internal
● Alias: read.bsfiles
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rescale
(Package: VanillaICE) :
Rescale a numeric vector
Rescale a numeric vector
● Data Source:
BioConductor
● Keywords: manip
● Alias: rescale
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rowModes
(Package: VanillaICE) :
Robust statistics for matrices
Compute the column-wide or row-wise mode of numeric matrices
● Data Source:
BioConductor
● Keywords:
● Alias: colModes, rowMAD, rowModes
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segs
(Package: VanillaICE) :
Accessor for the HMM segments
Accessor to obtain all segments from the HMM.
● Data Source:
BioConductor
● Keywords:
● Alias: segs, segs,HMM-method
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snpArrayAssays
(Package: VanillaICE) :
Create an assays object from log R ratios and B allele frequencies
This function is exported primarily for internal use by other BioC packages.
● Data Source:
BioConductor
● Keywords:
● Alias: snpArrayAssays
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sourcePaths
(Package: VanillaICE) :
Accessor for file paths containing SNP-level summaries
Files containing SNP-level summaries for log R ratios, B allele frequencies, and genotypes – one sample per subject – are required.
● Data Source:
BioConductor
● Keywords:
● Alias: sourcePaths, sourcePaths,ArrayViews-method
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Retrieve genomic location of SNPs
● Data Source:
BioConductor
● Keywords:
● Alias: start,oligoSnpSet-method
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state-methods
(Package: VanillaICE) :
Accessor for the Viterbi state path
The states are represented as integers: 1=homozygous deletion, 2=hemizygous deletion, 3=diploid normal heterozygosity, 4=diploid region of homozygosity, 5=single copy gain, 6=two or more copy gain.
● Data Source:
BioConductor
● Keywords:
● Alias: state,Viterbi-method, state-methods
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sweepMode
(Package: VanillaICE) :
Sweep the modal log R ratio (by row or column) from a matrix of log
This function simplifies the process of sweeping the modal log R ratio from the rows or columns of a SnpArrayExperiment object. It is most useful when a large number of samples (more than 10) are available and the dataset is a collection of germline samples. We assume that the samples are from a single batch and that the modal value will be a robust estimate of the mean log R ratio for diploid copy number. Variation in the modal estimates between markers is presumed to be attributable to probe effects (e.g., differences hybridization efficiency/PCR do to sequence composition). For sex chromosomes, one should apply this function separately to men and women and then recenter the resulting matrix according to the expected copy number.
● Data Source:
BioConductor
● Keywords:
● Alias: sweepMode, sweepMode,SnpArrayExperiment-method
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