class.cghRaw: Class to contain and describe raw or normalized array...

In tgac-vumc/CGHbase: CGHbase: Base functions and classes for arrayCGH data analysis.

Description

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.

Extends

Directly extends class eSet.

Creating Objects

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.

Slots

Inherited from eSet:

assayData:

Contains matrices with equal dimensions, and with column number equal to 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:

See eSet

featureData:

An AnnotatedDataFrame with columns Chromosome, Start, and End containing array element position data.

experimentData:

See eSet

annotation:

See eSet

Methods

Class-specific methods.

copynumber(cghRaw), copynumber(cghRaw,matrix)<-

Access and set elements named copynumber in the AssayData-class slot.

chromosomes, bpstart, bpend

Access the chromosomal positions stored in featureData

plot

Create a plot containing log2ratios ordered by chromosomal position

See eSet for derived methods. Annotation functionality is not yet supported.

Author(s)

Sjoerd Vosse

See Also

eSet-class, cghSeg-class, cghCall-class

Examples

# 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)

tgac-vumc/CGHbase documentation built on May 31, 2019, 8:59 a.m.