CNV.genomeplot {conumee} | R Documentation |
Create CNV plot for the whole genome or chromosomes.
CNV.genomeplot(object, ...) ## S4 method for signature 'CNV.analysis' CNV.genomeplot(object, chr = "all", chrX = TRUE, chrY = TRUE, centromere = TRUE, detail = TRUE, main = NULL, ylim = c(-1.25, 1.25), set_par = TRUE, cols = c("red", "red", "lightgrey", "green", "green"))
object |
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... |
Additional parameters ( |
chr |
character vector. Which chromomsomes to plot. Defaults to |
chrX |
logical. Plot values for chrX? Defaults to |
chrY |
logical. Plot values for chrY? Defaults to |
centromere |
logical. Show dashed lines at centromeres? Defaults to |
detail |
logical. If available, include labels of detail regions? Defaults to |
main |
character. Title of the plot. Defaults to sample name. |
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 CNV plots for the whole genome or defined chromosomes. Bins are shown as dots, segments 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')