freadGDCfile {CNVScope}

Read GDC segmentation datafile for low-pass sequencing data.

Description

Reads a GDC segmetnation file and extract the segmetnation data.

Usage

freadGDCfile(
  file,
  fread_skip = NULL,
  format = "TARGET",
  CN_colname = "log2",
  sample_pattern = "[^_]+",
  sample_colname = NULL
)

Arguments

file

GDC file to be read

fread_skip

The number of metadata lines to be skipped(typically 14)

format

The format of the files (TCGA,TARGET, or custom).

CN_colname

The name of the column containing the copy number values.

sample_pattern

Regex pattern to obtain the sample ID from the filename.

sample_colname

Alternatively, a column can be specified with the sample ID on each line.

Value

input_tsv_with_sample_info A data frame containing the sample information extracted from the filename, including sample name & comparison type.

References

https://docs.gdc.cancer.gov/Encyclopedia/pages/TCGA_Barcode/

Examples

freadGDCfile(file =
system.file("extdata","somaticCnvSegmentsDiploidBeta_TARGET-30-PANRVJ_NormalVsPrimary.tsv",
package = "CNVScope"))