Description Objects from the Class Slots Methods Author(s) References Examples
The CGHdata class is built to store the dataset
Objects can be created by calls of the form new("CGHdata", Y)
.
Y
:dataframe containing recorded values. One column
per profile (of the same length), with patient IDs as column names. If the data contains
probeID, then one column of Y must be named probeID
. If the data contains the genomic position, then one
column of Y must be named genomic.position
. If the data
contains GC content of the probe then one column of Y must be named
GCcontent
.
The dataset is checked while constructing the class. If colnames are
not GCcontent
, genomic.position
, probeID
, all columns will be
considered as microarray signals.
Y
:Contains the data one field per patient (list)
probeID
:Contains the ID of each probe (factor)
genomic.position
:Contains the genomic position of each probe (numeric)
GCcontent
:Contains the GC content of each probe (numeric)
Accessor to slots of the class
to construct the class
Assesses the maximum number of segments per profile
Assesses the maximum total number of segments
Joint segmentation of multiple CGH profiles
Separate segmentation single CGH profiles
print class object
show class object
summary of class object
F. Picard, E. Lebarbier, M. Hoebeke, G. Rigaill, B. Thiam, S. Robin
Joint segmentation, calling and normalization of multiple CGH profiles, Biostatistics (2011)
1 2 3 4 5 | #set.seed(1)
#simul = simulprofiles(M=5,n=100,k.mean=2,SNR=5,lambda=1)
#CGHd = new("CGHdata",Y=simul$Y)
#show(CGHd)
#summary(CGHd)
|
Loading required package: parallel
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