msc.biomarkers.fill {Metabonomic}R Documentation

Fill Empty Spaces in Biomarker Matrix

Description

Fill empty spaces (NA's) in biomarker matrix created by msc.peaks.align. Transcription of msc.biomarkers.fill function of caMassClass

Usage

msc.biomarkers.fill(X, Bmrks, BinBounds, FillType = 0.9)

Arguments

X Spectrum data either in matrix format [nFeatures x nSamples] or in 3D array format [nFeatures x nSamples x nCopies]. Row names (rownames(X)) store M/Z mass of each row.
Bmrks biomarker matrix containing one sample per column and one biomarker per row
BinBounds position (mass) of left-most and right-most peak in each bin
FillType how to fill empty spaces in biomarker data?
* if 0<=FillType<=1 than fill spaces with quantile(probs=FillType). For example: if FillType=1/2 than medium will be used, if FillType=1 than maximum value will be used, if FillType=0.9 than maximum will be used after discarding 10 * if FillType<0 than empty spaces will not be filled and NA's will remain * if FillType==2 than X value closest to the center of the bin will be used * if FillType==3 empty spaces will be set to zero

Details

Transcription of masc.biomarkers.fill function of caMassClass

Value

Data in the same format and size as Bmrks

Author(s)

Jarek Tuszynski (SAIC) jaroslaw.w.tuszynski@saic.com

References

caMassClass http://finzi.psych.upenn.edu/R/library/caMassClass/html/00Index.html


[Package Metabonomic version 3.3.1 Index]