CNV.analysis-class {conumee} | R Documentation |
CNV analysis data of a single sample is stored in this class
## S4 method for signature 'CNV.analysis' show(object) ## S4 method for signature 'CNV.analysis' names(x) ## S4 replacement method for signature 'CNV.analysis' names(x) <- value ## S4 method for signature 'CNV.analysis' coef(object)
object |
|
x |
|
value |
Replacement names. |
Use CNV.fit
to create. Modified by CNV.bin
, CNV.detail
and CNV.segment
.
CNV.analysis
class.
Volker Hovestadt conumee@hovestadt.bio
# prepare library(minfiData) data(MsetEx) d <- CNV.load(MsetEx) anno <- CNV.create_anno() # create object x <- CNV.fit(query = d['GroupB_1'], ref = d[c('GroupA_1', 'GroupA_2', 'GroupA_3')], anno) # modify object x <- CNV.bin(x) x <- CNV.detail(x) x <- CNV.segment(x) # general information x show(x) # coefficients of linear regression coef(x) # show or replace sample name names(x) names(x) <- 'Sample 1' # output plots CNV.genomeplot(x) CNV.genomeplot(x, chr = 'chr6') #CNV.detailplot(x, name = 'MYCN') #CNV.detailplot_wrap(x) CNV.write(x, what = 'segments')