removeModification {SMITE} | R Documentation |
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.
removeModification(pvalue_annotation, mod_type = "methylation")
pvalue_annotation |
An S4 object of class PvalueAnnotation |
mod_type |
A character string that identifies a type of modification within a PvalueAnnotation. |
An S4 object of class PvalueAnnotation
N. Ari Wijetunga
annotateModification extractModification extractModSummary
##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))