| cghRaw {CGHcall} | 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-classphenoData:eSetfeatureData:AnnotatedDataFrame with columns
Chromosome, Start, and End containing array element position
data.experimentData:eSetannotation:eSetClass-specific methods.
copynumber(cghRaw), copynumber(cghRaw,matrix)<-copynumber in the AssayData-class
slot.chromosomes, bpstart, bpendfeatureData
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(Wilting)
rawcgh <- make_cghRaw(Wilting)
# plot the first sample
plot(rawcgh[,1])
# first three chromosomes
plot(rawcgh[chromosomes(rawcgh)==1,1])
# get the copynumber values of the third and fourth sample
log2ratios <- copynumber(rawcgh[,3:4])
# get the names of the samples
sampleNames(rawcgh)
# get the names of the array elements
featureNames(rawcgh)