missing.sim: Missing peaks generating procedure for simulation study

In GMSimpute: Generalized Mass Spectrum Missing Peaks Abundance Imputation

Description

missing.sim generates various types of missing peaks based on specified missing proportion.

Usage

missing.sim(complete.data, total.missing, random, pct.full,
  seednum = 365)

Arguments

complete.data	The full abundance matrix without missing value, with features in rows and samples in columns.
total.missing	A scalar or vector of proportions. It is the total percentage of missing peaks throughout the full matrix.
random	A scalar or vector of proportions. It is the percentage of random missing in all the missing peaks.
pct.full	A scalar for the percentage of alighned features (metabolites or peptides) without missing peaks.
seednum	The seed set for generating missing peaks index. Default seed is seednum=365.

Value

simulated.data	The list of all simulated scenarios
Labels	The description for each simulated scenario

Examples

data('tcga.bc.full')
# tcga.bc.full contains mass specturm abundance of 100 metabolites for 30 breast cancer 
# tumor and normal tissue samples without missing values.


simulated.data=missing.sim(tcga.bc.full,total.missing=c(0.2,0.4),random=c(0.3,0.5,0.7),pct.full=0.4)
# Generate missing (NA) values in full abundance matrix tcga.bc.full permuting all scenarios

GMSimpute documentation built on May 1, 2019, 10:13 p.m.