rc.feature.replace.na: rc.feature.replace.na

In RAMClustR: Mass Spectrometry Metabolomics Feature Clustering and Interpretation

rc.feature.replace.na

Description

replaces any NA (and optionally zero) values with small signal (20

Usage

rc.feature.replace.na(
  ramclustObj = NULL,
  replace.int = 0.1,
  replace.noise = 0.1,
  replace.zero = TRUE,
  which.data = c("MSdata", "MSMSdata")
)

Arguments

ramclustObj	ramclustObj containing MSdata with optional MSMSdata (MSe, DIA, idMSMS)
replace.int	default = 0.1. proportion of minimum feature value to replace NA (or zero) values with
replace.noise	default = 0.1. proportion ofreplace.int value by which noise is added via 'jitter'
replace.zero	logical if TRUE, any zero values are replaced with noise as if they were NA values
which.data	name of dataset

Details

noise is added by finding for each feature the minimum detected value, multiplying that value by replace.int, then adding (replace.int*replace.noise) noise. abs() is used to ensure no negative values result.

Value

ramclustR object with NA and zero values removed.

Author(s)

Corey Broeckling

References

Broeckling CD, Afsar FA, Neumann S, Ben-Hur A, Prenni JE. RAMClust: a novel feature clustering method enables spectral-matching-based annotation for metabolomics data. Anal Chem. 2014 Jul 15;86(14):6812-7. doi: 10.1021/ac501530d. Epub 2014 Jun 26. PubMed PMID: 24927477.

RAMClustR documentation built on Oct. 20, 2023, 5:08 p.m.