cptSlopeplot: Scatterplot representation of identified change points gene...

In BhaktiDwivedi/GISPA: GISPA: Method for Gene Integrated Set Profile Analysis

Description

This function will plot the average slopes estimated over all gene sets within each change point by data types

Usage

cptSlopeplot(gispa.output,feature,type,cpt)

Arguments

gispa.output	: A data matrix of between gene feature profile statistics for each feature with corrosponding identified changepoints. The row names should corrospond to genes or names to be displayed on y-axis
feature	: Analysis type i.e., one ('1'), two ('2') or three ('3') dimensional feature analysis.
type	: Type of data, e.g., EXP (default) for expression, VAR of variants, CNV for copy number change.
cpt	: Change point cutoff to be highlighted. The default is 1

Details

This function expects the output from GISPA function of GISPA package, and highlights the gene set slope profile in the selected changepoints

Value

Scatterplot illustrating the average slopes by change point to access the best gene set profile

Author(s)

Bhakti Dwivedi & Jeanne Kowalski

Examples

id <- 200 ## number of rows
s <- 3 ## number of columns
dm <- matrix(runif(id*s,0,10), nrow=id, ncol=s, 
                 dimnames=list(paste("gene", 1:id, sep=""), 
                 paste("sample", 1:s, sep="")))
changepoints <- sort(sample(1:2, id, replace=TRUE))
dm <- cbind(dm,changepoints)
cptSlopeplot(gispa.output=dm,feature=1,type="EXP",cpt=1)

BhaktiDwivedi/GISPA documentation built on June 23, 2020, 3:41 p.m.