CNV.segment {conumee} | R Documentation |
Segment bin values (wrapper of DNAcopy
package).
CNV.segment(object, ...) ## S4 method for signature 'CNV.analysis' CNV.segment(object, alpha = 0.001, nperm = 50000, min.width = 5, undo.splits = "sdundo", undo.SD = 2.2, verbose = 0, ...)
object |
|
... |
Additional parameters supplied to the |
alpha |
See details. Defaults to 0.001. |
nperm |
See details. Defaults to 50000. |
min.width |
See details. Defaults to 5. |
undo.splits |
See details. Defaults to 'sdundo'. |
undo.SD |
See details. Defaults to 2.2. |
verbose |
See details. Defaults to 0. |
This method is a wrapper of the CNA, segment, segments.summary and segments.p methods of the DNAcopy package. Please refer to the respective man pages for more detailed information. The default parameters of CNV.segment
override some of the default parameters of segment and are optimized for 450k data CNV analysis.
CNV.analysis
object.
Volker Hovestadt conumee@hovestadt.bio
# prepare library(minfiData) data(MsetEx) d <- CNV.load(MsetEx) data(detail_regions) anno <- CNV.create_anno(detail_regions = detail_regions) # 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'