A B C D E F G I K L M N O P R S T U misc
A | Compute average log-intensities / log-ratios |
A-method | Compute average log-intensities / log-ratios |
A-method | Class "CNSet" |
A<- | Compute average log-intensities / log-ratios |
A<--method | Compute average log-intensities / log-ratios |
A<--method | Class "CNSet" |
addFeatureAnnotation | Add genomic annotation (chromosome, position) for several SNP platforms. |
AffyExonPDInfo-class | Class "DBPDInfo" |
AffyExpressionPDInfo-class | Class "DBPDInfo" |
AffyGenePDInfo-class | Class "DBPDInfo" |
affyPlatforms | Available Affymetrix platforms for SNP arrays |
AffySNPCNVPDInfo-class | Class "DBPDInfo" |
AffySNPPDInfo-class | Class "DBPDInfo" |
AffySTPDInfo-class | Class "DBPDInfo" |
AffyTilingPDInfo-class | Class "DBPDInfo" |
allele | Class "AlleleSet" |
allele-method | Class "AlleleSet" |
allele-method | Class "CNSet" |
AlleleSet-class | Class "AlleleSet" |
annotatedDataFrameFrom-method | Class "ff_matrix" |
annotation-method | Class "DBPDInfo" |
annotationPackages | Annotation Packages |
B | Compute average log-intensities / log-ratios |
B-method | Compute average log-intensities / log-ratios |
B-method | Class "CNSet" |
B<- | Compute average log-intensities / log-ratios |
B<--method | Compute average log-intensities / log-ratios |
B<--method | Class "CNSet" |
baf | Miscellaneous generics. Methods defined in packages that depend on oligoClasses |
batch | The batch variable for the samples. |
batch-method | Class "CNSet" |
batchNames | The batch variable for the samples. |
batchNames-method | Methods for class AssayData in the oligoClasses package |
batchNames-method | Class "CNSet" |
batchNames<- | The batch variable for the samples. |
batchNames<--method | Methods for class AssayData in the oligoClasses package |
batchNames<--method | Class "CNSet" |
batchStatistics | Accessor for batch statistics uses for copy number estimation and storage of model parameters |
batchStatistics-method | Class "CNSet" |
batchStatistics<- | Accessor for batch statistics uses for copy number estimation and storage of model parameters |
batchStatistics<--method | Class "CNSet" |
bothStrands | Class "AlleleSet" |
bothStrands-method | Class "AlleleSet" |
calls | Accessors and methods for SnpSet objects |
calls-method | Accessors and methods for SnpSet objects |
calls-method | Methods for oligoSnpSet class |
calls<- | Accessors and methods for SnpSet objects |
calls<--method | Accessors and methods for SnpSet objects |
calls<--method | Methods for oligoSnpSet class |
callsConfidence-method | Methods for oligoSnpSet class |
callsConfidence<--method | Methods for oligoSnpSet class |
celfileDate | Cel file dates |
checkExists | Checks to see whether an object exists and, if not, executes the appropriate function. |
checkOrder | Checks whether a eSet-derived class is ordered by chromosome and physical position |
checkOrder-method | Class '"CopyNumberSet"' |
checkOrder-method | Accessors and methods for SnpSet objects |
chromosome | Accessors for eSet extensions |
chromosome-method | Classes in MinimumDistance for data on ranges |
chromosome-method | Accessors for eSet extensions |
chromosome2integer | Converts chromosome to integer |
chromosome<- | Accessors for eSet extensions |
chromosome<--method | Accessors for eSet extensions |
close | Open and close methods for matrices and numeric vectors |
close-method | Compute average log-intensities / log-ratios |
close-method | Class "CNSet" |
close-method | Open and close methods for matrices and numeric vectors |
closeff | Open and close methods for matrices and numeric vectors |
closeff-method | Open and close methods for matrices and numeric vectors |
cnConfidence | Methods for class CopyNumberSet. |
cnConfidence-method | Class '"CopyNumberSet"' |
cnConfidence-method | Methods for oligoSnpSet class |
cnConfidence<- | Methods for class CopyNumberSet. |
cnConfidence<--method | Class '"CopyNumberSet"' |
cnConfidence<--method | Methods for oligoSnpSet class |
CNSet-class | Class "CNSet" |
coerce,CNSet,oligoSnpSet | Class "CNSet" |
coerce-method | Class "CNSet" |
coerce-method | Utility functions for RangedData extensions for storing ranged data on copy number variants. |
coerce-method | Methods for oligoSnpSet class |
confs | Accessors and methods for SnpSet objects |
confs-method | Accessors and methods for SnpSet objects |
confs<- | Accessors and methods for SnpSet objects |
confs<--method | Accessors and methods for SnpSet objects |
copyNumber | Methods for class CopyNumberSet. |
copyNumber-method | Class '"CopyNumberSet"' |
copyNumber-method | Methods for oligoSnpSet class |
copyNumber<- | Methods for class CopyNumberSet. |
copyNumber<--method | Class '"CopyNumberSet"' |
copyNumber<--method | Methods for oligoSnpSet class |
CopyNumberSet-class | Class '"CopyNumberSet"' |
CopyNumberSet-methods | Methods for class CopyNumberSet. |
corr | Methods for class AssayData in the oligoClasses package |
corr-method | Class "CNSet" |
coverage2 | Utility functions for RangedData extensions for storing ranged data on copy number variants. |
coverage2-method | Classes in MinimumDistance for data on ranges |
createFF | Create ff objects. |
db | Get the connection to the SQLite Database |
db-method | Class "AlleleSet" |
db-method | Get the connection to the SQLite Database |
db-methods | Get the connection to the SQLite Database |
DBPDInfo-class | Class "DBPDInfo" |
delCluster | Cluster and large dataset management utilities. |
efsExample | ExpressionFeatureSet Object |
ExonFeatureSet-class | "FeatureSet" and "FeatureSet" Extensions |
ExpressionFeatureSet-class | "FeatureSet" and "FeatureSet" Extensions |
ExpressionPDInfo-class | Class "DBPDInfo" |
exprs-method | Accessor for the 'exprs' slot |
exprs-methods | Accessor for the 'exprs' slot |
FeatureSet-class | "FeatureSet" and "FeatureSet" Extensions |
featuresInRange | Find feature index in a genomic interval |
featuresInRange-method | Classes in MinimumDistance for data on ranges |
ffdf-class | Class "ffdf" |
ff_matrix-class | Class "ff_matrix" |
findOverlaps | Find markers that overlap with a query set of ranges |
findOverlaps-method | Find markers that overlap with a query set of ranges |
flags | Batch-level summary of SNP flags. |
flags-method | Methods for class AssayData in the oligoClasses package |
flags-method | Class "CNSet" |
GeneFeatureSet-class | "FeatureSet" and "FeatureSet" Extensions |
genomeBuild | Genome Build Information |
genomeBuild-method | Genome Build Information |
geometry | Array Geometry Information |
geometry-method | Array Geometry Information |
getA | Compute average log-intensities / log-ratios |
getA-method | Class "AlleleSet" |
getA-method | Compute average log-intensities / log-ratios |
getBar | Gets a bar of a given length. |
getCluster | Cluster and large dataset management utilities. |
getM | Compute average log-intensities / log-ratios |
getM-method | Class "AlleleSet" |
getM-method | Compute average log-intensities / log-ratios |
i2p | Functions to convert probabilities to integers, or integers to probabilities. |
initialize-method | Class "CNSet" |
initialize-method | Class '"CopyNumberSet"' |
initialize-method | Class "DBPDInfo" |
initialize-method | "FeatureSet" and "FeatureSet" Extensions |
initialize-method | Class "SnpSuperSet" |
initialize-method | Methods for oligoSnpSet class |
initializeBigMatrix | Initialize big matrices/vectors. |
initializeBigVector | Initialize big matrices/vectors. |
is.ffmatrix | Check if object is an ff-matrix object. |
isPackageLoaded | Check if package is loaded. |
isSnp | Accessors for eSet extensions |
isSnp-method | Accessors for eSet extensions |
kind | Array type |
kind-method | Array type |
ldPath | Set/check large dataset options. |
ldSetOptions | Set/check large dataset options. |
ldStatus | Set/check large dataset options. |
length-method | Number of samples for FeatureSet-like objects. |
length-methods | Number of samples for FeatureSet-like objects. |
list.celfiles | List CEL files. |
list_or_ffdf-class | Class "ffdf" |
locusLevelData | Basic data elements required for the HMM |
lrr | Miscellaneous generics. Methods defined in packages that depend on oligoClasses |
manufacturer | Manufacturer ID for FeatureSet-like objects. |
manufacturer-method | Manufacturer ID for FeatureSet-like objects. |
manufacturer-methods | Manufacturer ID for FeatureSet-like objects. |
NgsExpressionPDInfo-class | Class "DBPDInfo" |
NgsTilingPDInfo-class | Class "DBPDInfo" |
nu | Methods for class AssayData in the oligoClasses package |
nu-method | Methods for class AssayData in the oligoClasses package |
nu-method | Class "CNSet" |
ocLapply | lapply-like function that parallelizes code when possible. |
ocProbesets | Cluster and large dataset management utilities. |
ocSamples | Cluster and large dataset management utilities. |
oligoSet | An example instance of oligoSnpSet class |
oligoSnpSet-class | Methods for oligoSnpSet class |
open | Open and close methods for matrices and numeric vectors |
open-method | Compute average log-intensities / log-ratios |
open-method | Class "CNSet" |
open-method | Open and close methods for matrices and numeric vectors |
openff | Open and close methods for matrices and numeric vectors |
openff-method | Open and close methods for matrices and numeric vectors |
order | Methods for CopyNumberSet objects |
order-method | Methods for CopyNumberSet objects |
p2i | Functions to convert probabilities to integers, or integers to probabilities. |
parStatus | Checks if oligo/crlmm can use parallel resources. |
pdPkgFromBioC | Get packages from BioConductor. |
phi | Methods for class AssayData in the oligoClasses package |
phi-method | Methods for class AssayData in the oligoClasses package |
phi-method | Class "CNSet" |
platform | Platform Information |
platform-method | Platform Information |
platform-methods | Platform Information |
pmFragmentLength | Information on Fragment Length |
pmFragmentLength-method | Information on Fragment Length |
pmFragmentLength-methods | Information on Fragment Length |
position | Accessors for eSet extensions |
position-method | Accessors for eSet extensions |
RangedDataCBS | Utility functions for RangedData extensions for storing ranged data on copy number variants. |
RangedDataCBS-class | Classes in MinimumDistance for data on ranges |
RangedDataCNV | Utility functions for RangedData extensions for storing ranged data on copy number variants. |
RangedDataCNV-class | Classes in MinimumDistance for data on ranges |
RangedDataCopyNumber-class | Classes in MinimumDistance for data on ranges |
RangedDataHMM | Utility functions for RangedData extensions for storing ranged data on copy number variants. |
RangedDataHMM-class | Classes in MinimumDistance for data on ranges |
requireAnnotation | Helper function to load packages. |
requireClusterPkg | Package loaders for clusters. |
requireClusterPkgSet | Package loaders for clusters. |
sampleNames-method | Classes in MinimumDistance for data on ranges |
sampleNames-method | Sample names for FeatureSet-like objects |
sampleNames-methods | Sample names for FeatureSet-like objects |
sampleNames<--method | Utility functions for RangedData extensions for storing ranged data on copy number variants. |
scqsExample | SnpCnvQSet Example |
se.exprs-method | Accessor for the 'exprs' slot |
setCluster | Cluster and large dataset management utilities. |
sfsExample | SnpFeatureSet Example |
show-method | Class "CNSet" |
show-method | Class "DBPDInfo" |
show-method | "FeatureSet" and "FeatureSet" Extensions |
sigma2-method | Class "CNSet" |
SnpCnvFeatureSet-class | "FeatureSet" and "FeatureSet" Extensions |
SNPCNVPDInfo-class | Class "DBPDInfo" |
SnpFeatureSet-class | "FeatureSet" and "FeatureSet" Extensions |
SNPPDInfo-class | Class "DBPDInfo" |
SnpSuperSet-class | Class "SnpSuperSet" |
splitIndicesByLength | Tools to distribute objects across nodes or by length. |
splitIndicesByNode | Tools to distribute objects across nodes or by length. |
sqsExample | SnpQSet Example |
state | Utility functions for RangedData extensions for storing ranged data on copy number variants. |
state-method | Classes in MinimumDistance for data on ranges |
tau2-method | Class "CNSet" |
TilingFeatureSet-class | "FeatureSet" and "FeatureSet" Extensions |
TilingFeatureSet2-class | "FeatureSet" and "FeatureSet" Extensions |
TilingPDInfo-class | Class "DBPDInfo" |
todf-method | Classes in MinimumDistance for data on ranges |
updateObject-method | Class "CNSet" |
[-method | Class "CNSet" |