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**VanillaICE**: A Hidden Markov Model for high throughput genotyping arrays**sourcePaths**: Accessor for file paths containing SNP-level summaries

# Accessor for file paths containing SNP-level summaries

### Description

Files containing SNP-level summaries for log R ratios, B allele frequencies, and genotypes – one sample per subject – are required.

### Usage

1 | ```
sourcePaths(object)
``` |

### Arguments

`object` |
an |

### Examples

1 |

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- acf2: Calculate lag10 autocorrelation
- ArrayViews-class: ArrayViews class, constructor, and methods
- baumWelchUpdate: Function for updating parameters for emission probabilities
- calculateEmission: Calculate the emission probabilities for the 6-state HMM
- cnvFilter: Filter the HMM-derived genomic ranges for copy number...
- CopyNumScanParams: Parameters for parsing source files containing SNP-array...
- doUpdate: Helper function to determine whether to update the HMM...
- dropDuplicatedMapLocs: Drop markers on the same chromosome having the same genomic...
- dropSexChrom: Filter sex chromosomes
- emission: Methods to set and get emission probabilities
- emissionParam: Accessor for parameters used to compute emission...
- EmissionParam-methods: A parameter class for computing Emission probabilities
- FilterParam-class: Container for the common criteria used to filtering genomic...
- filters: Accessor for HMM filter parameters
- getExampleSnpExperiment: Create an example SnpArrayExperiment from source files...
- getHmmParams: Accessor for HMM model parameters
- HMM: Container for the segmented data and the 6-state HMM model...
- hmm2: Fit a 6-state HMM to log R ratios and B allele frequencies...
- HmmGRanges-methods: Accessor for copy number state
- HMMList: Constructor for 'HMMList' class
- HMMList-class: Class, constructor, and methods for representing HMM results...
- HmmParam: Constructor for HmmParam class
- hmmResults: Example output from the hidden markov model
- HmmTrellisParam: Constructor for HmmTrellisParam class
- IdiogramParam-class: Constructor for IdiogramParam objects
- IdiogramParams-class: Paramater class for plotting idiograms
- IO: Accessors for objects of class ArrayViews
- isHeterozygous: Assess whether genotype is heterozygous based on BAFs
- LogLik: Constructor for LogLik class
- LogLik-class: Classes and methods for storing/getting log-likelihoods from...
- LowLevelSummaries: Accessor for SNP genotypes
- matrixOrNULL-class: A class allowing matrix or NULL objects
- NA_filter: Remove SNPs with NAs in any of the low-level estimates
- numberFeatures: The number of SNP/nonpolymorphic probes contained in a...
- parsedPath: Complete path to directory for keeping parsed files
- parseSourceFile: Function for parsing GenomeStudio files
- plotting: Lattice-style plots for granges and SnpArrayExperiment...
- probability: Accessor for probability filter
- rescale: Rescale a numeric vector
- robust-statistics: Robust statistics for matrices
- segs: Accessor for the HMM segments
- snpArrayAssays: Create an assays object from log R ratios and B allele...
- SnpArrayExperiment-class: A RangedSummarizedExperiment-derived class of marker-level...
- snp_exp: An example SnpArrayExperiment
- SnpExperiment: Constructor for SnpArrayExperiment
- SnpGRanges: An extension to GRanges for representing SNPs
- sourcePaths: Accessor for file paths containing SNP-level summaries
- start-oligoSnpSet-method: Retrieve genomic location of SNPs
- state-methods: Accessor for the Viterbi state path
- sweepMode: Sweep the modal log R ratio (by row or column) from a matrix...
- threshold: Threshold numeric values
- TransitionParam: Constructor for TransitionParam class
- updateHmmParams: Run the Baum-Welch algorithm to update HMM parameters
- VanillaICE: A hidden markov model for detection of germline copy number...
- viewports: Default viewports for plotting CNV data with lattice-style...
- Viterbi-methods: Show method for objects of class 'Viterbi'