mQTL.NMR

Version: 1.12.0

Website

https://www.bioconductor.org/packages/release/bioc/html/mQTL.NMR.html

Description

mQTL.NMR, a bioconductor package, provides a complete mQTL analysis pipeline for 1H NMR data, including processing, statistical analysis between metabolites and QTL and visualisation. NMR data should be preprocessed before being loaded into mQTL.NMR (FT, apodization, calibration, phasing and baseline correction). A number of normalisation approaches are provided: constant sum, constant noise, linear baseline and probabilistic quotient normalisation. Two scaling options are available: Pareto and autoscaling. Recursive segment wise peak alignment (RSPA) is used for peak alignment. There are two approaches to reduce dimensionality for mapping metabolites to QTLs: bucketing and statistical recoupling of variables (SRV). For animal crosses, the extended Haley-Knott regression method is used. For human mapping, simple linear regression is used to map SNPs to metabolites. Other covariants such as sex and age can also be taken into account in the model, due to the use of GenABEL.

Functionality

• Statistical Analysis

Instrument Data Type

• NMR/1H NMR

Approaches

Computer Skills

Advanced

Software Type

R Package

Interface

Command line interface

Operating System (OS)

• Unix/Linux
• Mac OS
• Windows

Language

R

Dependencies

R ≥ 2.15.0, qtl, GenABEL

Input Formats - Open

Text file

Input Formats - Proprietary

N/A

Published

2015

Last Updated

2017

License

Artistic-2.0

Paper

http://www.ncbi.nlm.nih.gov/pubmed/25803548

PMID

25803548