dt_to_385k: Converts aCGH data to hg18 385k design

In arnijohnsen/arjtools: Collection of tools used in copy number variation analysis

Description

Converts aCGH data to a hg18 385k design. Each input probe is mapped to its nearest output probe in the 385k design. If multiple inputs match to a single output, their mean is computed. If no input matches to a 385k probe, an NA value is returned for that output.

Usage

dt_to_385k(dt, assembly = "hg18")

Arguments

dt	data.table with aCGH data. First two colums should be names chrom and pos and contain information about the location of input probes. Chromosomes should be names "chr1", "chrY", etc. The remaining columns are interpreted as samples with the column name denoting the sample name.
assembly	String specifying assembly of input data. Can take values "hg18" (default) or "hg17" (in which case, design must match hg17 385k design).

Value

data.table with mapped data. First two colums are chrom and pos and contain information about the location of input probes. The remaining columns are mapped data for each sample.

arnijohnsen/arjtools documentation built on May 10, 2019, 1:45 p.m.