cghRaw {CGHbase} | R Documentation |
Container for aCGH data and experimental
metadata. cghRaw
class is derived from
eSet
, and requires a matrix named copynumber
as
assayData member. Furthermore, columns named Chromosome
, Start
, and End
are required as featureData members, containing feature position information.
Directly extends class eSet
.
new('cghRaw',
phenoData = [AnnotatedDataFrame],
experimentData = [MIAME],
annotation = [character],
copynumber = [matrix],
featureData = [AnnotatedDataFrame],
...)
make_cghRaw
is a function to convert a dataframe or textfile to
an object of class cghRaw
. The input should be either a dataframe
or a tabseparated textfile (textfiles must contain a header). The first
three columns should contain the name, chromosome and position in bp for
each array target respectively. The chromosome and position column must
contain numbers only. Following these is a column with log2 ratios for
each of your samples. If the input type is a textfile, missing values
should be represented as 'NA' or an empty field.
Inherited from eSet
:
assayData
:nrow(phenoData)
. assayData
must contain a matrix
copynumber
with rows represening array probes
and columns representing samples. Additional matrices of
identical size (e.g., representing measurement errors) may
also be included in assayData
. Class:AssayData-class
phenoData
:eSet
featureData
:AnnotatedDataFrame
with columns
Chromosome
, Start
, and End
containing array element position
data.experimentData
:eSet
annotation
:eSet
Class-specific methods.
copynumber(cghRaw)
, copynumber(cghRaw,matrix)<-
copynumber
in the AssayData-class
slot.chromosomes
, bpstart
, bpend
featureData
See eSet
for derived methods. Annotation functionality is not yet supported.
Sjoerd Vosse
eSet-class
, cghSeg-class
, cghCall-class
# create an instance of cghRaw new("cghRaw") # create an instance of cghRaw from a dataframe data(WiltingData) cghobj <- cghRaw(WiltingData) # plot the first sample plot.cghRaw(cghobj[,1]) # first three chromosomes plot.cghRaw(cghobj[chromosomes(cghobj)==1,1]) # get the copynumber values of the third and fourth sample log2ratios <- copynumber(cghobj[,3:4]) # get the names of the samples sampleNames(cghobj) # get the names of the array elements featureNames(cghobj)