formSampleMatrixFromRawGDCData {CNVScope} | R Documentation |
Form sample matrix from GDC copy number data files.
Description
Reads a GDC segmetnation files, adds sample information, and forms a data matrix of samples and bins of a specified size.
Arguments
tcga_files |
GDC files to be read |
format |
file format, TCGA or TARGET. |
binsize |
the binsize, in base pairs (default 1Mb or 1e6). This value provides a good balance of resolution and speed with memory sensitive applications. |
freadskip |
the number of lines to skip in the GDC files, typically 14 (the first 13 lines are metadata and the first is a blank line in NBL data). Adjust as needed. |
debug |
debug mode enable (allows specific breakpoints to be checked). |
chromosomes |
A vector of chromosomes to be used. Defaults to chr1-chrX, but others can be added e.g. chrY or chrM for Y chromosome or mitochondrial DNA. Format expected is a character vector, e.g. c("chr1", "chr2", "chr3"). |
sample_pat |
Pattern used to extract sample name from filename. Use "" to use the filename. |
sample_col |
The name of the sample column (for custom format input). |
chrlabel |
The name of the chromosome column (for custom format input). |
startlabel |
The name of the start column (for custom format input). |
endlabel |
The name of the end column (for custom format input). |
Value
A dataframe containing the aggregated copy number values, based on the parameters provided.
Examples
#Pipeline examples would be too large to include in package checks.
#please see browseVignettes("CNVScope") for a demonstration.