diggit-methods: Basic methods for class diggit

In diggit: Inference of Genetic Variants Driving Cellular Phenotypes

Description

This document lists a series of basic methods for the class diggit

Usage

## S4 method for signature 'diggit'
print(x, pval = 0.05)

## S4 method for signature 'diggit'
show(object)

## S4 method for signature 'diggit'
exprs(object)

## S4 method for signature 'diggit'
diggitCNV(x)

## S4 method for signature 'diggit'
diggitRegulon(x)

## S4 method for signature 'diggit'
diggitMindy(x)

## S4 method for signature 'diggit'
diggitFcnv(x)

## S4 method for signature 'diggit'
diggitMR(x)

## S4 method for signature 'diggit'
diggitViper(x)

## S4 method for signature 'diggit'
diggitAqtl(x)

## S4 method for signature 'diggit'
diggitConditional(x)

## S4 method for signature 'diggit'
summary(object)

## S4 method for signature 'diggit'
head(x, rows = 4, cols = 4)

## S4 method for signature 'diggit'
mindyFiltering(x, mr = 0.01, mr.adjust = c("none", "fdr",
  "bonferroni"))

Arguments

x	Object of class diggit
pval	P-value threshold for the conditional analysis
object	Object of class diggit
rows	Integer indicating the maximum number of rows to show
cols	Integer indicating the maximum number of columns to show
mr	Either a numerical value between 0 and 1 indicating the p-value threshold for the Master Regulator (MR) selection, or a vector of character strings listing the MRs
mr.adjust	Character string indicating the multiple hypothesis test correction for the MRs

Value

print returns summary information about the diggit object

show returns summary information about the object of class diggit

exprs returns the ExpressionSet object containing the expression profile data

diggitCNV returns a matrix containing the CNV data

diggitRegulon returns a regulon object containing the transcriptional interactome

diggitMindy returns a regulon object containing the post-translational interactome

diggitFcnv returns a vector of p-values for the F-CNVs

diggitMR returns a vector of master regulators NES

diggitViper returns a matrix of VIPER results

diggitAqtl returns a matrix of aQTLs (p-value)

diggitConditional returns a list containing the conditional analysis results

summary returns the integrated results from the conditional analysis

head returns a list containing a reduced view for an object of class diggit

mindyFiltering returns a diggit class object with CNV and aQTL slots filtered to contain only MINDy post-translational modulators of the MRs

Examples

data(gbm.expression, package="diggitdata")
data(gbm.cnv, package="diggitdata")
data(gbm.aracne, package="diggitdata")
dobj <- diggitClass(expset=gbmExprs, cnv=gbmCNV, regulon=gbmTFregulon)
print(dobj)
show(dobj)
exprs(dobj)
diggitCNV(dobj)[1:3, 1:3]
diggitRegulon(dobj)
diggitMindy(dobj)
diggitFcnv(dobj)
diggitMR(dobj)
diggitViper(dobj)
diggitAqtl(dobj)
diggitConditional(dobj)
head(dobj)
data(gbm.expression, package="diggitdata")
data(gbm.cnv, package="diggitdata")
data(gbm.mindy, package="diggitdata")
dobj <- diggitClass(expset=gbmExprs, cnv=gbmCNV, mindy=gbmMindy)
dobj <- fCNV(dobj)
dobj
dobj <- mindyFiltering(dobj, mr=c("STAT3", "CEBPD"))
dobj

diggit documentation built on Nov. 8, 2020, 8:18 p.m.