makePvalueObject: Function to make a PvalueObject within a PvalueAnnotation
In SMITE: Significance-based Modules Integrating the Transcriptome and Epigenome

Description Usage Arguments Details Value Author(s) See Also Examples

Having annotated modifications and expression data this function will assemble a PvalueObject within the slot "score_data" of a PvalueAnnotation. This is a necessary step before being able to run downstrem functions.

1	makePvalueObject(pvalue_annotation, effect_directions = NULL)

`pvalue_annotation`	An S4 object of class PvalueAnnotation
`effect_directions`	A character vector with optional names specifying "increase" Modification is expected to increase as expression increase "decrease" Modification is expected to descrease as expression decreases "bidirectional" No direction is assumed between modification and direction

The specified relationship between the modification and expression will be stored and then used when scoring.

An S4 object of class PvalueAnnotation with a slot for score_data filled it

N.Ari Wijetunga

makePvalueAnnotation

#NOTE: Commented out in example, please see vignette for more details##
options(stringsAsFactors=FALSE)

data(methylationdata)
methylation <- methylation[-which(is.na(methylation[, 5])), ]
#methylation[, 5] <- replace(methylation[, 5],methylation[, 5] == 0, 
#min(subset(methylation[, 5], methylation[, 5] != 0), na.rm=TRUE))

#data(curated_expressiondata)
#data(hg19_genes_bed)
#data(histone_h3k4me1)

#test_annotation<-makePvalueAnnotation(data=hg19_genes, 
#other_data=list(h3k4me1=h3k4me1), gene_name_col=5,other_tss_distance=5000)

#fill in expression data
#test_annotation<-annotateExpression(test_annotation, expression_curated)


#fill in methylation data
#this step takes ~10 minutes
#test_annotation<-annotateModification(test_annotation, methylation, 
#weight_by=c(promoter="distance",body="distance",h3k4me1="distance"),
#verbose=TRUE, mod_corr=FALSE)

#create a pvalue object that will count the effect of the h3k4me1 as
#bidirectional
#test_annotation<-makePvalueObject(pvalue_annotation=test_annotation, 
#effect_directions=c(methylation_promoter="decrease",
#methylation_body="decrease", methylation_h3k4me1="bidirectional"))