snr.FC: snr.FC - Fold Changes

In galder-max/GSEAlite: GSEA lite performs simple GSEA analysis with few useful functions

Description

snr.FC computes mean fold changes between two classes in a matrix of expression. A 2-level factor is used to compare two classes (unpaired). If no factor is given as input the matrix is considered as a paired difference in log2 between two groups.

Usage

snr.FC(m, o = NULL)

Arguments

m	matrix of expressions. columns represent samples, rows are genes.
o	2-class factor where length(o) equals ncol(m). If left to NULL, m is considered as a paired difference between two classes.

Value

returns a vector of size nrow(m) correspondig to the fold changes for each gene/row.

Author(s)

[e-mail]

See Also

snr.SNR

Examples

##creates a matrix of 10000 rows/genes and 10 columns/samples
m<-matrix(rnorm(10*10000),10000,10)


##creates a factor vector of length nrow(m)=10
o<-as.factor(c(rep(1,5),rep(2,5)))

##print results
head(snr.FC(m,o))
head(snr.FC(m))

##compare the SNR metric to the fold changes
plot(snr.SNR(m,o),snr.FC(m,o),xlab="SNR",ylab="FC",main="Comparison
between the two metrics",pch=".")

##same as above but paired
plot(snr.SNR(m,o=NULL),snr.FC(m,o=NULL),xlab="SNR",ylab="FC",main="Comparison
between the two metrics",pch=".")

galder-max/GSEAlite documentation built on Jan. 30, 2021, 10:50 p.m.