Dexpress: Identifying the differentially expressed proteins and...

In Mathlida/comPath: Integrating proteomic and phosphoproteomic data for pathway analysis

Description

Identifying the differentially expressed proteins and phosphoproteins and the differentially expressed degree (fold change) of all the proteins and phosphoproteins

Usage

Dexpress(exprs,phosexprs,case,ctrl)

Arguments

exprs	The protein expression values which have been .
phosexprs	The phosphoproteinexpression values
case	A vector of names of case samples
ctrl	A vector of names of ctrl samples

Details

If this function is called, two queries will appear in the console: "Have you normalized exprs dataset? Yes(y) or NO(n)?" & "Have you normalized phosexprs dataset? Yes(y) or NO(n)?". If you type "y", Student’s t-test will be used to get the differential expression of proteome or phosphoproteome. If you type "n", ‘Mann-Whitney’ test will be used to get the differential expression. A Bonferroni correction (p < 0.05) will be applied following the two kinds of tests. The differentially expressed degree (fold change) of all the proteins and phosphoproteins is between case and control samples. The input of the function are proteome and phosphoproteome expression data matrix and two vector of sample names (case & control).

Value

allpro	all of the expressed proteins
allphos	all of the expressed phosphoproteins
DEpro	Differentilly expressed proteins
DEphos	Differentilly expressed phosphoproteins
fcpro	the fold chage of DEpros
fcphos	the fold chage of DEphos

Author(s)

Jie Ren, Jing Li

Examples

data(exprs)
data(phosexprs)
case=c("A1","A2","A3","A4","A5","A6","A7","A8","A9","A10")
ctrl=c("B1","B2","B3")
DEexpression=Dexpress(exprs,phosexprs,case,ctrl)
summary(DEexpression)

Mathlida/comPath documentation built on May 23, 2019, 5:03 p.m.