Error message in getTargetAnnotationStats

[abcosta]

Hi,

I am trying to use genomation and methylKit to analyze some RRBS data. I identified the identified the significantly differentially methylated cytosines (q-value threshold of 0.01 and a minimum change in percent methylation of 25%) and used for the gene annotation analysis a .gtf file. I ended up using two scripts (gtfToGenePred and genePredToBed) from http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/ to convert my .gtf file to .bed Everything seems to have worked fine until I tried to use "getTargetAnnotationStats" which gives me a error message (please see below): #R code

mydiff25 <- getMethylDiff(mydiff, difference = 25, qvalue = 0.01) nrow(mydiff25) [1] 178

library(genomation) gene.obj<-readTranscriptFeatures("ensGene_revised-sorted.bed") Reading the table... Calculating intron coordinates... Calculating exon coordinates... Calculating TSS coordinates... Calculating promoter coordinates... Outputting the final GRangesList...

ann=annotateWithGeneParts(as(mydiff25, "GRanges"), gene.obj) ann Summary of target set annotation with genic parts Rows in target set: 178

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percentage of target features overlapping with annotation:
promoter exon intron intergenic
3.93 6.74 35.39 57.87
percentage of target features overlapping with annotation: (with promoter > exon > intron precedence):
promoter exon intron intergenic
3.93 4.49 33.71 57.87
percentage of annotation boundaries with feature overlap: promoter exon intron
0.03 0.00 0.01
summary of distances to the nearest TSS:
Min. 1st Qu. Median Mean 3rd Qu. Max.
132 4327 13174 233837 53026 5049539

getTargetAnnotationStats(ann,percentage=TRUE,precedence=TRUE) Error in getTargetAnnotationStats(ann, percentage = TRUE, precedence = TRUE) : unused arguments (ann, percentage = TRUE, precedence = TRUE)

Could you help me to figure out what is the issue?

Any help on this is much appreciated. Cheers