CNV.detailplot {conumee} | R Documentation |
Create CNV plot for detail region.
CNV.detailplot(object, ...) ## S4 method for signature 'CNV.analysis' CNV.detailplot(object, name, yaxt = "l", ylim = c(-1.25, 1.25), set_par = TRUE, cols = c("red", "red", "lightgrey", "green", "green"))
object |
|
... |
Additional parameters ( |
name |
character. Name of detail region to plot. |
yaxt |
character. Include y-axis? |
ylim |
numeric vector. The y limits of the plot. Defaults to |
set_par |
logical. Use recommended graphical parameters for |
cols |
character vector. Colors to use for plotting intensity levels of bins. Centered around 0. Defaults to |
This method provides the functionality for generating detail regions CNV plots. Probes are shown as dots, bins are shown as lines. See parameters for more information.
NULL
.
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/modify object x <- CNV.segment(CNV.detail(CNV.bin(CNV.fit(query = d['GroupB_1'], ref = d[c('GroupA_1', 'GroupA_2', 'GroupA_3')], anno)))) # output plots CNV.genomeplot(x) CNV.genomeplot(x, chr = 'chr6') CNV.detailplot(x, name = 'PTEN') CNV.detailplot_wrap(x) # output text files CNV.write(x, what = 'segments') CNV.write(x, what = 'detail') CNV.write(x, what = 'bins') CNV.write(x, what = 'probes')