extractModification: Extract some or all loaded modifications or a the summary of...

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

Description

After having loaded modifications into a PvalueAnnotation, these functions can be used to display the GRanges with the modification of interest, or the data frame containg a summary of the combined effects.

Usage

extractModification(pvalue_annotation, mod_type = "methylation")
extractModSummary(pvalue_annotation)

Arguments

pvalue_annotation	An s4 object of calss PvalueAnnotation
mod_type	A string or character vector that must match one or more of the loaded modifications. If NULL (DEFAULT) then it will show all modifications.

Value

A GRanges object containing the modification(s) of interest or a data frame with a summary of the combined p-values and effects

Author(s)

N. Ari Wijetunga

See Also

extractExpression annotateModificaiton removeModification

Examples

##NOTE: Comment out in exmaple see vignette for more detailed usage ##

## Load genome bed file ##
data(hg19_genes_bed)

## Load curated DNA methylation bed file ##
#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))

## Create a PvalueAnnotation with defaults for promoter size##
test_annotation<-makePvalueAnnotation(data=hg19_genes, gene_name_col=5)

## Load DNA methylation into PvalueAnnotation ##
#test_annotation <- annotateModification(pvalue_annotation=test_annotation, 
#methylation, weight_by=c(promoter="distance", body="distance"), verbose=TRUE,
#mod_corr=FALSE, mod_type="methylation")

## Extract GRanges with modification data ##
#extractModification(pvalue_annotation=test_annotation)

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