freadGDCfile | R Documentation |
Reads a GDC segmetnation file and extract the segmetnation data.
freadGDCfile( file, fread_skip = NULL, format = "TARGET", CN_colname = "log2", sample_pattern = "[^_]+", sample_colname = NULL )
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. |
input_tsv_with_sample_info A data frame containing the sample information extracted from the filename, including sample name & comparison type.
https://docs.gdc.cancer.gov/Encyclopedia/pages/TCGA_Barcode/
freadGDCfile(file = system.file("extdata","somaticCnvSegmentsDiploidBeta_TARGET-30-PANRVJ_NormalVsPrimary.tsv", package = "CNVScope"))
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