impact: Evaluate the different impacts betwween proteins and...

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

Description

A function evaluates and visualizes the different impacts between proteins and phosphoproteins on a disturbed pathway.

Usage

impact(DEexpression)

Arguments

DEexpression

Six variables including all expressed proteins and phosphoproteins, their differential expression and the fold change of the differential expression.

Details

A function evaluates and visualizes the different impacts between proteins and phosphoproteins on a disturbed pathway. The function evaluates the difference by comparing z-scored fold change of proteins and phosphoproteins included in the pathway.If the difference exists in a pathway, z-scored fold change of expressed proteins and phosphoproteins of the pathway will be recorded and a boxplot and a KEGG pathway map will be produced to show the difference. In the pathway mapping figure, the left part of rectangle representing the z-scored fold change of proteins and right part representing phosphoproteins. Red represents up-regulated and yellow represents down-regulated. If the gene does not expressed, the color of the rectangle is white. A file named "plot" will be created in the work directory and all the generated 'png' figures will be included in.

Value

DiffPath	The number of pathways in which proteins and phosphoproteins contribute differently
NODiffPath	The number of pathways in which proteins and phosphoproteins contribute almost equally
Dlist	the detail of "DiffPath"
Slist	the detail of "NODiffPath"

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)
Impacts <- impact(DEexpression)
summary(Impacts)

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