delRep: delRep()

In LipidomicsR: Elegant Tools for Processing and Visualization of Lipidomics Data

delRep()

Description

A function to delete specific number of replicates, the replicates causing largest standard deviation will be deleted.

Usage

delRep(data, group, m, method = "PCA", show.del = FALSE)

Arguments

data	A dataframe storing concentration of lipids between different samples. The column name should be the sample name and the row name should be the lipid type. The class of column name and row name should be "character". The class of values should be "numeric". The row names are recommended to be in a form like "PL(14:0/20:1)" or "LPL(16:1)".
group	Vector. The group information, recommended to be generated with groupXpert()
m	The number of replicates you want to delete.
method	The method to find the worst replicates, can be "PCA" or "Euclidean". Default value is "PCA".
show.del	Whether to show deleted columns. Default value is FALSE.

Value

A new dataframe deleting replicates which cause the largest SD.

Examples

WT_1=rnorm(n=5,mean=0.3,sd=0.1)
WT_2=rnorm(n=5,mean=0.3,sd=0.1)
WT_3=rnorm(n=5,mean=0.3,sd=0.1)
WT_4=rnorm(n=5,mean=0.3,sd=0.1)
KO_1=rnorm(n=5,mean=0.3,sd=0.1)
KO_2=rnorm(n=5,mean=0.3,sd=0.1)
KO_3=rnorm(n=5,mean=0.3,sd=0.1)
KO_4=rnorm(n=5,mean=0.3,sd=0.1)
data=data.frame(WT_1,WT_2,WT_3,WT_4,KO_1,KO_2,KO_3,KO_4)
rownames(data)=c("LPC(16:0)","PC(14:0/16:1)","PC(18:1/18:1)","PE(18:0/20:1)","PS(20:1/20:1)")
m=1
group=colnames(data)
names(group)=rep(c("WT","KO"),each=4)
delRep(data,group,m)

LipidomicsR documentation built on May 29, 2024, 8:59 a.m.