makeGRangesListFromCopyNumber: Make a GRangesList from TCGA Copy Number data

In waldronlab/TCGAmisc: TCGA utility functions for data management

Make a GRangesList from TCGA Copy Number data

Description

makeGRangesListFromCopyNumber allows the user to convert objects of class data.frame or S4Vectors::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).

Usage

makeGRangesListFromCopyNumber(
  df,
  split.field,
  names.field = "Hugo_Symbol",
  ...
)

Arguments

df	A data.frame or DataFrame class object. list class objects are coerced to data.frame or DataFrame.
split.field	A character vector of length one indicating the column to be used as sample identifiers
names.field	A character vector of length one indicating the column to be used as names for each of the ranges in the data
...	Additional arguments to pass on to GenomicRanges::makeGRangesListFromDataFrame

Value

A GRangesList class object

Examples

library(GenomicDataCommons)

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")
barcode <- barcode[["associated_entities.entity_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

waldronlab/TCGAmisc documentation built on Dec. 19, 2024, 2:10 p.m.