| print,diggit-method {diggit} | R Documentation |
This document lists a series of basic methods for the class diggit
## 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"))
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 |
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
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