makePvalueObject: Function to make a PvalueObject within a PvalueAnnotation

In AJEinstein/SMITE: Significance-based Modules Integrating the Transcriptome and Epigenome

Description

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.

Usage

makePvalueObject(pvalue_annotation, effect_directions = NULL)

Arguments

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

Details

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

Value

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

Author(s)

N.Ari Wijetunga

See Also

makePvalueAnnotation

Examples

#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"))

AJEinstein/SMITE documentation built on Oct. 23, 2021, 7:44 a.m.