GEList-class {snapCGH} | R Documentation |
A list based class for storing the location of points of interest
within the data set following the segmentation step. Events include whole chromosomal gains and losses,
aberrations, transitions, amplifications and their respective counts
and sizes. They are
generally created by running the function findGenomicEvents
.
Objects should contain the following list components:
num.transitions : | matrix of dimensions maxChrom by number of samples. It contains number of transitions that were recorded on a given chromosome for a given sample. |
num.amplifications : | matrix of dimensions maxChrom by number of samples It contains number of amplifications that were recorded on a given chromosome for a given sample. |
num.aberrations : | matrix of dimensions maxChrom by number of samples. It contains number of focal aberrations that were recorded on a given chromosome for a given sample. |
num.outliers : | matrix of dimensions maxChrom by number of samples. It contains number of outliers that were recorded on a given chromosome for a given sample. |
num.transitions.binary : | binary matrix of dimensions maxChrom by number of samples. Non-zero entry indicates whether 1 or more transitions were recorded on a given chromosome for a given sample. |
num.amplifications.binary : | binary matrix of dimensions maxChrom by number of samples. Non-zero entry indicates whether 1 or more amplifications were recorded on a given chromosome for a given sample. |
num.aberrations.binary : | binary matrix of dimensions maxChrom by number of samples. Non-zero entry indicates whether 1 or more focal aberrations were recorded on a given chromosome for a given sample. |
num.outliers.binary : | binary matrix of dimensions maxChrom by number of samples. Non-zero entry indicates whether 1 or more outliers were recorded on a given chromosome for a given sample. |
whole.chrom.gain.loss : | matrix of dimensions maxChrom by number of samples. Positive entry indicates that a given chromosome was gained in a given sample, negative entry indicates that a given chromosome was lost in a given sample, 0 entry is normal chromosome and NA marks chromosomes with one or more transition. |
size.amplicons : | matrix of dimensions maxChrom by number of samples. Reports size of a given chromosome that is amplified (kb units) in a given sample. |
num.amplicons : | matrix of dimensions maxChrom by number of samples. Reports number of disjoint amplicons on a given chromosome for a given sample. |
outliers : | list containing 3 matrices of dimensions number of clones by number of samples. See findOutliers . |
aberrations : | list containing a matrix of dimensions number of clones by number of samples. See findAberrations . |
transitions : | list containing 2 matrices of dimensions number of clones by number of samples. See findTranslocations . |
amplifications : | list containing a matrix of dimensions number of clones by number of samples. See findAmplifications . |
Mike Smith
SegList
plotSegmentationStates