apply.ns.cna.thresh: Determine the copy number (CN) values from pre-defined ratio...

In uclahs-cds/public-R-NanoStringNormCNV: Helper Functions to Normalize NanoString CNV Data

Determine the copy number (CN) values from pre-defined ratio thresholds

Description

Determine the copy number values from count ratios using pre-defined thresholds

Usage

apply.ns.cna.thresh(ratio.data, cna.thresh = c(0.4, 1.5, 2.5, 3.5))

Arguments

ratio.data	A gene by sample data-frame of tumour:normal ratios. See output of NanoStringNormCNV:::get.tumour.normal.ratio
cna.thresh	A 4-element vector with the tumour-normal thresholds to call homozygous deletions, heterozygous deletions, single copy gains, and multi-copy gains. Default values (0.4, 1.5, 2.5, 3.5) are derived from NanoString recommendations.

Details

Determine the copy number values (0, 1, 2, 3, 4) of each probe from raw tumour:normal count ratios using pre-defined thresholds.

Value

A gene by sample data-frame of copy number values

Author(s)

Cindy Yao and Emilie Lalonde

References

See NanoString website for PDFs on analysis guidelines: https://www.nanostring.com/support/product-support/support-documentation

The NanoString assay is described in the paper: Fortina, P. & Surrey, S. Digital mRNA profiling. Nature Biotechnology 26, 293-294 (2008).

See Also

NanoStringNormCNV:::apply.kd.cna.thresh

uclahs-cds/public-R-NanoStringNormCNV documentation built on May 31, 2024, 9:09 p.m.