Dingxia,

Please try this instead,

TSS = getBM(c("gene", "chromosome_name", "chromosome_start",
            "chromosome_end", "chromosome_strand"), mart = mart)
TSS = unique(TSS[!is.na(TSS[,3]),])
Annotation = RangedData(IRanges(start = as.numeric(TSS[, 3]), end = as.numeric(TSS[,
            4]), names = as.character(TSS[, 1])), strand = TSS[,
            5], space = as.character(TSS[,
            2]))

Best regards,

Julie

On 8/29/12 2:41 PM, "Dingxia Feng" <fengdxia@iastate.edu> wrote:

Hi, Zhuli,

I have to trouble to run the getAnnotation code. This is how I did it:

> library(ChIPpeakAnno)
> mart=useMart("WS220",dataset="wormbase_gene")
> Annotation = getAnnotation(mart,featureType="TSS")
Error in getBM(c("ensembl_gene_id", "chromosome_name", "start_position",  :
  Invalid attribute(s): ensembl_gene_id, start_position, end_position, strand, description
Please use the function 'listAttributes' to get valid attribute names

So it looks the getAnnotation function recognize the ensemble database, not the WS220. The reason I need WS220 is that I used it in the previous alignment. So julie, is there a way to get this annotation work with WS220 in ChIPpeakAnno? Thanks.

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