| AllAccessors {rCGH} | R Documentation |
"rCGH" Accessor Functions Methods for extracting information from an object of
class "rCGH".
Each of the below methods are simply convenience functions which extract the
corresponding slots (as the name of each method suggests) from an object of
class "rCGH".
## S4 method for signature 'rCGH' getInfo(object, item = NULL) ## S4 method for signature 'rCGH' getCNset(object) ## S4 method for signature 'rCGH' getParam(object) ## S4 method for signature 'rCGH' getSegTable(object, minLen = NULL)
object |
: An object of class |
item |
: character. Can be one, or a vector of items.
When |
minLen |
: numeric. The mininal length for a segment, in Kb.
When |
getInfo(object, item = NULL): character.
getCNset(object): a data frame.
getParam(object): a list of parameters.
getSegTable(object, minLen = NULL): a data frame.
"rCGH"getInfo(object, item = NULL): returns the values of the specified items, all the information otherwise.
getCNset(object): returns the full by-probe dataset.
getParam(object): returns the analysis parameters.
getSegTable(object, minLen = NULL): returns the segmentation table - one row per segment.
Frederic Commo
filePath <- system.file("extdata", "Agilent4x180K.txt.bz2", package = "rCGH")
cgh <- readAgilent(filePath, sampleName = "Agilent4x180K", labName = "myLab")
# Getting all the information
getInfo(cgh)
# Getting specific items
getInfo(cgh, c("sampleName", "labName"))