restriction.fragmentation.qc: Perform QAQC using restriction fragmentation controls

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

Perform QAQC using restriction fragmentation controls

Description

Perform QAQC using restriction fragmentation controls and create diagnostic figures

Usage

	restriction.fragmentation.qc(raw.data)

Arguments

raw.data

A gene by sample data-frame of raw NanoString counts of restriction fragmentation probes. First three column names must be 'CodeClass', 'Name', and 'Accession', followed by sample IDs

Details

Restriction fragmentation controls check for proper denaturation and digestion of DNA in AluI digested samples. The following results are expected: a) probes C and D with counts of > 200 if DNA had correctly denatured prior to digestion and b) probe ratios (C+D / A+B) of > 10 if DNA digestion was complete. The user is warned if low count or low ratio samples are detected.
Diagnostic plot is saved as a tiff file to the working directory.

Value

A data-frame containing 1) C and D probe mean counts, 2) A and B probe mean counts, and 3) C+D / A+B ratios

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).

Examples

## Not run: 
	# load raw data
	data(NanoString.DNA.raw);

	# run QC
	qc.results <- restriction.fragmentation.qc(raw.data = NanoString.DNA.raw);

## End(Not run)

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