calcFractionalCopyNumbers |
Calculation of fractional copy numbers for the CNVs and CNV regions. |
calcFractionalCopyNumbers-method |
Calculation of fractional copy numbers for the CNVs and CNV regions. |
calcIntegerCopyNumbers |
Calculation of integer copy numbers for the CNVs and CNV regions. |
calcIntegerCopyNumbers-method |
Calculation of integer copy numbers for the CNVs and CNV regions. |
cn.mops |
Copy number detection in NGS data. |
CNVDetectionResult |
Class "CNVDetectionResult" |
CnvDetectionResult |
Class "CNVDetectionResult" |
cnvdetectionresult |
Class "CNVDetectionResult" |
CNVDetectionResult-class |
Class "CNVDetectionResult" |
cnvr |
This generic function returns CNV regions of a CNV detection method stored in an instance of 'CNVDetectionResult-class'. |
cnvr-method |
This generic function returns CNV regions of a CNV detection method stored in an instance of 'CNVDetectionResult-class'. |
CNVRanges |
Genomic locations and indices of the simulated CNVs. |
cnvs |
This generic function returns CNVs of a CNV detection method stored in an instance of 'CNVDetectionResult-class'. |
cnvs-method |
This generic function returns CNVs of a CNV detection method stored in an instance of 'CNVDetectionResult-class'. |
exomecn.mops |
Copy number detection in exome sequencing data. |
exomeCounts |
Read counts from exome sequencing for CNV detection |
getReadCountsFromBAM |
Calculation of read counts from BAM files. |
getSegmentReadCountsFromBAM |
Calculation of read counts from BAM files for predefined segments. |
gr |
This generic function returns the genomic ranges of a CNV detection method stored in an instance of 'CNVDetectionResult-class'. |
gr-method |
This generic function returns the genomic ranges of a CNV detection method stored in an instance of 'CNVDetectionResult-class'. |
haplocn.mops |
Copy number detection in NGS data of haploid samples. |
individualCall |
This generic function returns the individual calls of a CNV detection method stored in an instance of 'CNVDetectionResult-class'. |
individualCall-method |
This generic function returns the individual calls of a CNV detection method stored in an instance of 'CNVDetectionResult-class'. |
iniCall |
This generic function returns the informative/non-informative call of a CNV detection method stored in an instance of 'CNVDetectionResult-class'. The I/NI call is a measure for a genomic segment across all samples, whether this segment is a CNV region (informative) or a normal genomic region (non-informative). |
iniCall-method |
This generic function returns the informative/non-informative call of a CNV detection method stored in an instance of 'CNVDetectionResult-class'. The I/NI call is a measure for a genomic segment across all samples, whether this segment is a CNV region (informative) or a normal genomic region (non-informative). |
integerCopyNumber |
This generic function returns the integer copy numbers of a CNV detection method stored in an instance of 'CNVDetectionResult-class'. |
integerCopyNumber-method |
This generic function returns the integer copy numbers of a CNV detection method stored in an instance of 'CNVDetectionResult-class'. |
localAssessments |
This generic function returns the local assessments, i.e. signed individual informative/non-informative calls, of a CNV detection method stored in an instance of 'CNVDetectionResult-class'. For other CNV detection methods this can be (log-) ratios or z-scores. |
localAssessments-method |
This generic function returns the local assessments, i.e. signed individual informative/non-informative calls, of a CNV detection method stored in an instance of 'CNVDetectionResult-class'. For other CNV detection methods this can be (log-) ratios or z-scores. |
makeRobustCNVR |
Calculates robust CNV regions. |
makeRobustCNVR-method |
Calculates robust CNV regions. |
normalizeChromosomes |
Normalization of NGS data. |
normalizedData |
This generic function returns the normalized data of a CNV detection method stored in an instance of 'CNVDetectionResult-class'. |
normalizedData-method |
This generic function returns the normalized data of a CNV detection method stored in an instance of 'CNVDetectionResult-class'. |
normalizeGenome |
Normalization of NGS data |
params |
This generic function returns the parameters of a CNV detection method stored in an instance of 'CNVDetectionResult-class'. |
params-method |
This generic function returns the parameters of a CNV detection method stored in an instance of 'CNVDetectionResult-class'. |
plot-method |
Plots a CNVDetectionResult |
plot-methods |
Plots a CNVDetectionResult |
posteriorProbs |
This generic function returns the posterior probabilities of a CNV detection method stored in an instance of 'CNVDetectionResult-class'. The posterior probabilities are represented as a three dimensional array, where the three dimensions are segment, copy number and individual. |
posteriorProbs-method |
This generic function returns the posterior probabilities of a CNV detection method stored in an instance of 'CNVDetectionResult-class'. The posterior probabilities are represented as a three dimensional array, where the three dimensions are segment, copy number and individual. |
referencecn.mops |
Copy number detection in NGS data with in a control versus cases setting. |
sampleNames |
This generic function returns the sample names of a CNV detection method stored in an instance of 'CNVDetectionResult-class'. |
sampleNames-method |
This generic function returns the sample names of a CNV detection method stored in an instance of 'CNVDetectionResult-class'. |
segment |
Fast segmentation of CNV calls. |
segmentation |
This generic function returns segmentation of a CNV detection method stored in an instance of 'CNVDetectionResult-class'. |
segmentation-method |
This generic function returns segmentation of a CNV detection method stored in an instance of 'CNVDetectionResult-class'. |
segplot |
Visualization of a CNV detection result. |
segplot-method |
Visualization of a CNV detection result. |
show-method |
Displays the result object of a copy number detection method. |
show-methods |
Displays the result object of a copy number detection method. |
singlecn.mops |
Copy number detection in NGS data with in a setting in which only one sample is available |
X |
A simulated data set for CNV detection from NGS data. |
XRanges |
A simulated data set for CNV detection from NGS data. |