GISPA: Gene Integrates Set Profile Analysis

Description Usage Arguments Value

View source: R/GISPA.R

Description

Identifies gene sets with a similar a prior defined profile using any combination of three feature or data types

Usage

1
GISPA(feature,f.sets,g.set,ref.samp.idx,comp.samp.idx,f.profiles,cpt.data,cpt.method,cpt.max)

Arguments

feature

: Analysis type i.e., one ('1'), two ('2') or three ('3') dimensional feature analysis.

f.sets

: A list of ExpressionSet data objects corrosponding to a data type

g.set

: A GeneSet from an ExpressionSet to subset the f.sets for analysis purposes. 'geneIds' should corrospond to the gene names. Default is null, i.e., genome-wide analysis

ref.samp.idx

: Reference sample column index on which to determine the gene set profile. The default is 3

comp.samp.idx

: The other two relative sample column index against which the profile is being determined. The default is 4 and 5

f.profiles

: A vector of the desired direction of genomic change (or profile) corrosponding to each data type. The values are "up" or "down" for increased and decreased gene set profile, respectively

cpt.data

: Identify changepoints for data using variance (cpt.var), mean (cpt.mean) or both (meanvar). Default is cpt.var.

cpt.method

: Choice of single or multiple changepoint model. Default is "BinSeg".

cpt.max

: The maximum number of changepoints to search for using "BinSeg" method. Default is 60. This number is dependent on the number of input data points

Value

The returned value is a data matrix including the original data along with between gene profile statistics and identified changepoints.


GISPA documentation built on May 2, 2018, 3:59 a.m.

Related to GISPA in GISPA...