extractModification {SMITE} | R Documentation |
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.
extractModification(pvalue_annotation, mod_type = "methylation") extractModSummary(pvalue_annotation)
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. |
A GRanges object containing the modification(s) of interest or a data frame with a summary of the combined p-values and effects
N. Ari Wijetunga
extractExpression annotateModificaiton removeModification
##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)