extractModification {SMITE} | R Documentation

## Extract some or all loaded modifications or a the summary of combined effects

### 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)

[Package SMITE version 1.14.0 Index]