formSampleMatrixFromRawGDCData: Form sample matrix from GDC low-pass segmentation datafiles.

In jamesdalg/HiCNV: A Versatile Toolkit for Copy Number Variation Relationship Data Analysis and Visualization

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.

Value

sample_aggregated_segvals A dataframe containing the aggregated segmentation values, based on the parameters provided.

Examples

#Pipeline examples would be too large to include in package checks.
#please see browseVignettes("HiCNV") for a demonstration.

jamesdalg/HiCNV documentation built on May 9, 2019, 5:05 a.m.