Make a GRangesList from TCGA Copy Number data — makeGRangesListFromCopyNumber • TCGAutils

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)

UUIDtoBarcode(names(fname), from_type = "file_id")
#>                                file_id associated_entities.entity_submitter_id
#> 1 27942c4d-57d1-43c2-a27f-ce4ed46f75a2            TCGA-NH-A5IV-01A-42D-A36W-01

cndata <- read.delim(fname[[1L]])

makeGRangesListFromCopyNumber(
    df = cndata,
    split.field = "GDC_Aliquot",
    keep.extra.columns = TRUE
)
#> GRangesList object of length 1:
#> $`9ffe4929-b7aa-4e04-9876-56b1c4b33139`
#> GRanges object with 222 ranges and 2 metadata columns:
#>         seqnames              ranges strand | Num_Probes Segment_Mean
#>            <Rle>           <IRanges>  <Rle> |  <integer>    <numeric>
#>     [1]        1       62920-4874007      * |       1887       0.0317
#>     [2]        1     4883463-5054493      * |        174      -0.6952
#>     [3]        1    5060514-20995776      * |       9503       0.0053
#>     [4]        1   20997998-21094512      * |         43      -0.6860
#>     [5]        1   21096482-72297687      * |      31164       0.0110
#>     ...      ...                 ...    ... .        ...          ...
#>   [218]        X  81419945-155734427      * |      41590       0.0074
#>   [219]        X 155736972-155952689      * |         16      -0.8036
#>   [220]        Y     2782397-6195105      * |        762      -1.9317
#>   [221]        Y    6195308-21578726      * |       5481      -2.1922
#>   [222]        Y   21582050-56872112      * |        387      -1.9747
#>   -------
#>   seqinfo: 24 sequences from an unspecified genome; no seqlengths
#>