A B C D E F G I K L M N O P R S T
A | Compute average log-intensities / log-ratios |
A-method | Compute average log-intensities / log-ratios |
A<- | Compute average log-intensities / log-ratios |
A<--method | Compute average log-intensities / log-ratios |
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" |
AlleleSet-class | Class "AlleleSet" |
annotation-method | Class "DBPDInfo" |
annotationPackages | Annotation Packages |
B | Compute average log-intensities / log-ratios |
B-method | Compute average log-intensities / log-ratios |
B<- | Compute average log-intensities / log-ratios |
B<--method | Compute average log-intensities / log-ratios |
bothStrands | Class "AlleleSet" |
bothStrands-method | Class "AlleleSet" |
CA | Class "CNSet" |
CA-method | Class "CNSet" |
CA<- | Class "CNSet" |
CA<--method | Class "CNSet" |
calls | Accessors for Calls and Confidences on a SnpSet object |
calls-method | Accessors for Calls and Confidences on a SnpSet object |
calls-method | Methods for oligoSnpSet class |
calls<- | Accessors for Calls and Confidences on a SnpSet object |
calls<--method | Accessors for Calls and Confidences on a SnpSet object |
calls<--method | Methods for oligoSnpSet class |
callsConfidence-method | Methods for oligoSnpSet class |
callsConfidence<--method | Methods for oligoSnpSet class |
CB | Class "CNSet" |
CB-method | Class "CNSet" |
CB<- | Class "CNSet" |
CB<--method | Class "CNSet" |
celfileDate | Cel file dates |
chromosome | Accessors for eSet extensions |
chromosome-method | Accessors for eSet extensions |
chromosome2integer | Converts chromosome to integer |
chromosome<- | Accessors for eSet extensions |
chromosome<--method | Accessors for eSet extensions |
close | Compute average log-intensities / log-ratios |
close-method | Compute average log-intensities / log-ratios |
cnConfidence | Methods for class CopyNumberSet. |
cnConfidence-method | Methods for class CopyNumberSet. |
cnConfidence-method | Methods for oligoSnpSet class |
cnConfidence<- | Methods for class CopyNumberSet. |
cnConfidence<--method | Methods for class CopyNumberSet. |
cnConfidence<--method | Methods for oligoSnpSet class |
CNSet-class | Class "CNSet" |
confs | Accessors for Calls and Confidences on a SnpSet object |
confs-method | Accessors for Calls and Confidences on a SnpSet object |
confs<- | Accessors for Calls and Confidences on a SnpSet object |
confs<--method | Accessors for Calls and Confidences on a SnpSet object |
copyNumber | Methods for class CopyNumberSet. |
copyNumber-method | Methods for class CopyNumberSet. |
copyNumber-method | Methods for oligoSnpSet class |
copyNumber<- | Methods for class CopyNumberSet. |
copyNumber<--method | Methods for class CopyNumberSet. |
copyNumber<--method | Methods for oligoSnpSet class |
CopyNumberSet-methods | Methods for class CopyNumberSet. |
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 |
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 |
initialize-method | Class "CNSet" |
initialize-method | Methods for 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. |
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" |
ocLapply | lapply-like function that parallelizes code when possible. |
ocProbesets | Cluster and large dataset management utilities. |
ocSamples | Cluster and large dataset management utilities. |
oligoSnpSet-class | Methods for oligoSnpSet class |
open | Compute average log-intensities / log-ratios |
open-method | Compute average log-intensities / log-ratios |
parStatus | Checks if oligo/crlmm can use parallel resources. |
pdPkgFromBioC | Get packages from BioConductor. |
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 | Accessor to position information |
position-method | Accessors for eSet extensions |
requireAnnotation | Helper function to load packages. |
requireClusterPkg | Package loaders for clusters. |
requireClusterPkgSet | Package loaders for clusters. |
sampleNames-method | Sample names for FeatureSet-like objects |
sampleNames-methods | Sample names for FeatureSet-like objects |
scqsExample | SnpCnvQSet Example |
se.exprs-method | Accessor for the 'exprs' slot |
setCluster | Cluster and large dataset management utilities. |
sfsExample | SnpFeatureSet Example |
show-method | Class "DBPDInfo" |
show-method | "FeatureSet" and "FeatureSet" Extensions |
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 |
TilingFeatureSet-class | "FeatureSet" and "FeatureSet" Extensions |
TilingFeatureSet2-class | "FeatureSet" and "FeatureSet" Extensions |
TilingPDInfo-class | Class "DBPDInfo" |