RUVphospho: RUV for phosphoproteomics data normalisation

In SydneyBioX/phosphoR: A set of methods and tools for comprehensive analysis of phosphoproteomics data

Description

This is a wrapper implementation of RUVIII for phosphoproteomics data normalisation. This function will call tailImpute function to impute all the missing values (if there is any) in the phosphoproteomics data for applying RUVIII. It will then return the normalised values for quantified phosphosites and remove imputed values.

Usage

RUVphospho(Y, M, ctl, k=NULL, ...)

Arguments

Y	a matrix with rows correspond to phosphosites and columns correspond to samples.
M	is the design matrix as defined in RUVIII.
ctl	is the stable phosphosites (or negative controls as defined in RUVIII).
k	is the number of unwanted factors as defined in RUVIII.
...	additional parameters that may be passed to RUVIII.

SydneyBioX/phosphoR documentation built on May 20, 2019, 12:58 a.m.