makeGRangesListFromCopyNumber {TCGAutils} | R Documentation |
makeGRangesListFromCopyNumber
allows the user to convert objects of
class data.frame
or DataFrame to a
GRangesList. It includes additional features specific to TCGA
data such as, hugo symbols, probe numbers, segment means, and
ucsc build (if available).
makeGRangesListFromCopyNumber( df, split.field, names.field = "Hugo_Symbol", ... )
df |
A |
split.field |
A |
names.field |
A |
... |
Additional arguments to pass on to makeGRangesListFromDataFrame |
A GRangesList class object
library(GenomicDataCommons) library(magrittr) manif <- files() %>% filter(~ cases.project.project_id == "TCGA-COAD" & data_type == "Copy Number Segment") %>% manifest(size = 1) fname <- gdcdata(manif$id) barcode <- UUIDtoBarcode(names(fname), from_type = "file_id")$cases.submitter_id cndata <- read.delim(fname[[1L]], nrows = 10L) cngrl <- makeGRangesListFromCopyNumber(cndata, split.field = "GDC_Aliquot", keep.extra.columns = TRUE) names(cngrl) <- barcode GenomeInfoDb::genome(cngrl) <- extractBuild(fname[[1L]]) cngrl