createCNSummary {beadarraySNP} | R Documentation |
Create a summary object of the genomic copy number states in a sample of segmented data
createCNSummary(object, sample, dnaIndex=1, subsample = "OPA")
object |
SNPSetIllumina object after segmentation segmentate |
sample |
SampleName or index of the sample for which to create the summary |
dnaIndex |
Measured DNA index of the sample |
subsample |
factor or column name in featureData slot |
The segments within a sample are assigned a copy number value. When the inferred
slot
in assayData
is empty, all segments will be set to 2. Otherwise the values are recovered
from the inferred
slot. Gender is taken into account for the sex chromosomes.
list with the following elements
dnaIndex |
same as parameter dnaIndex |
CN.total.nrm |
Total expected copynumber for a 'normal' specimen ~ 2*featurecount |
states |
data.frame with columns opa, count ,intensity, copynumber |
This list can be used as the cn.sum
argument for plotGoldenGate4OPA, alterCN,
getDNAindex
and setRealCN
Jan Oosting
segmentate, alterCN, plotGoldenGate4OPA