compSetSBR: Add SBR matrix to the experiment data object

In kroemerlab/GRMeta: Processing MetX data

Description

Compute signal to blank matrix and add to the metaboSet data object

Usage

compSetSBR(obj, thresh = 1, SidBlank = NULL, what = "Height", newname = NULL, fct = median)

Arguments

obj	Experiment object
thresh	Threshold used for NAs and censoring low intensities
SidBlank	Vector of Sids used for blank calculations
what	Matrix on which SBR calculation is performed
newname	Name of the SBR matrix to be added - if NULL returns the matrix rather than the object
fct	Function used to compute the blank level for each analyte

Value

metaboSet object or list of SBR matrix and the normalisation factor

Author(s)

David Enot [e-mail]

Examples

(testfiles=list.files(system.file( package = "GRMeta"),pattern = "txt$",full.names = TRUE))
mydata=loadAgilentData(ifile =testfiles[1])

mydata$Sid

newdata=compSetSBR(mydata,thresh=10,SidBlank=c( "Bl_prerun-eau_1","Bl_prerun-eau_1b", "Bl_prerun-matrice_4","Bl_postrun-matrice_4"),fct=median)
mydata

newdata=compSetSBR(mydata,thresh=10,SidBlank=NULL,newname="SBR")
newdata
head(newdata$Annot$SBR)

## return the SBR matrix  and not the metaboSet object
newdata=compSetSBR(mydata,thresh=10,SidBlank=NULL)
str(newdata)

kroemerlab/GRMeta documentation built on March 25, 2020, 11:32 a.m.