dat.oncoPrint Enables creation of a matrix used to generate an OncoPrint heatmap.

dat.oncoPrint Enables creation of a matrix used to generate an OncoPrint heatmap.

dat.oncoPrint(gen.dat, clin.dat = NULL)

Arguments

gen.dat	A binary matrix or dataframe, with patients as rows and features as columns. Note that the names of the columns must end in ".Del" or ".Amp" to recognize copy number alterations. (see create.bin.matrix for more details on this format).
clin.dat	An optional clinical file, including only the features the user wishes to add to the plot. Default is NULL.

Value

mat : a matrix ready to be plotted using plot.Oncoprint().

Examples

library(gnomeR)
patients <- as.character(unique(mut$Tumor_Sample_Barcode))
bin.mut <- binmat(patients = patients,maf = mut,mut.type = "SOMATIC",
SNP.only = FALSE,include.silent = FALSE, specify.plat = FALSE)
gen.dat <- bin.mut[1:500,
names(sort(apply(bin.mut,2, sum),decreasing = TRUE))[1:15]]
dat <- dat.oncoPrint(gen.dat)
## adding clinical ##
clin.patients.dat <-
clin.patients[match(abbreviate(rownames(gen.dat),
strict = TRUE, minlength = 9),
clin.patients$X.Patient.Identifier),] %>%
dplyr::rename(DMPID = X.Patient.Identifier,
 Smoker = Smoking.History) %>%
  dplyr::select(DMPID, Sex,Smoker) %>%
  dplyr::filter(!is.na(DMPID)) %>%
  dplyr::distinct(DMPID,.keep_all = TRUE)
gen.dat <- gen.dat[match(clin.patients.dat$DMPID,
abbreviate(rownames(gen.dat),strict = TRUE, minlength = 9)),]
clin.patients.dat <- clin.patients.dat %>%
dplyr::mutate(DMPID = as.character(DMPID)) %>%
  tibble::column_to_rownames('DMPID')
rownames(gen.dat) <- rownames(clin.patients.dat)
dat <- dat.oncoPrint(gen.dat = gen.dat,clin.dat = clin.patients.dat)