removeModification {SMITE} | R Documentation

## A function to "unload" a modification that has already been added.

### Description

After using the annotateModification function to load a modification into a PValue annotation, you may wish to remove a modification or reannotate one, which requires removing it first.

### Usage

    removeModification(pvalue_annotation, mod_type = "methylation")

### Arguments

`pvalue_annotation` | An S4 object of class PvalueAnnotation
`mod_type` | A character string that identifies a type of modification within a PvalueAnnotation.

### Value

An S4 object of class PvalueAnnotation

### Author(s)

N. Ari Wijetunga

### See Also

annotateModification extractModification extractModSummary

### Examples

    ##NOTE: Commented out in example. ##
    ## Please see vignette for more detailed usage information ##

    ## 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))

    #meth1<-methylation

    ## make second curated test methylation bed file ##

    #meth2<-methylation

    ## 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(annotation=test_annotation,
    #mod_data=meth1, weight_by=c(promoter="distance",body="distance"),verbose=TRUE,
    #mod_corr=TRUE,mod_type="methylation")

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

    ## Load second dataset bed file ##
    #test_annotation<-annotateModification(pvalue_annotation=test_annotation,
    #mod_data=meth2, weight_by=c(promoter="distance",body="distance"),
    #verbose=TRUE, mod_corr=TRUE,mod_type="hydroxy")

    ## Extract GRanges with both modification dataset loaded ##
    #head(extractModification(test_annotation,"hydroxy"))

    ## Unload DNA hydroxymethylation form PvalueAnnotation ##

    #test_annotation<-removeModification(pvalue_annotation=test_annotation,
                                        #mod_type="hydroxy")

    ## Extract GRanges to see only one modification dataset loaded ##
    #head(extractModification(pvalue_annotation=test_annotation))

[Package SMITE version 1.14.0 Index]