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