Creates a heatmap of copy number profiles from segment files.

facets.heatmap(
  seg = NULL,
  filenames = NULL,
  path = NULL,
  patients = NULL,
  min.purity = 0.3,
  epsilon = 0.005,
  ordered = NULL,
  outcome = NULL,
  adaptive = FALSE
)

Arguments

seg

a segmentation file containing the segmentation information of multiple patients

filenames

the names of the segment files to be loaded and processed (Note must end in ".Rdata").

path

the relative path to the files folder from your current directory

patients

the names of the patients of the respective filenames. Default simply 1 to number of files.

min.purity

the minimum purity of the sample required to be kept in the final dataset. Default is 0.3.

epsilon

level of unions when aggregating segments between

ordered

order in which patients should be printed. Default NUll leads to hierarchical clustering.

outcome

for seg file only, if outcome associated with study it will be printed along the x axis for each patient

adaptive

CNregions option to create adaptive segments

Value

p a heatmap corresponding to the segment files inputted

Examples

library(gnomeR) library(dplyr) library(dtplyr) patients <- as.character(unique(mut$Tumor_Sample_Barcode))[1:1000] patients.seg <- as.character(unlist(clin.sample %>% filter(Sample.Identifier %in% patients, as.numeric(as.character(Tumor.Purity)) > 30) %>% select(Sample.Identifier))) facet <- facets.heatmap(seg = seg, patients=patients.seg[0:100])
#> The "ward" method has been renamed to "ward.D"; note new "ward.D2"
facet$p