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R package for genomic feature analysis and visualization
http://bioinformatics.mdc-berlin.de/genomation/
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Error during annotateWithGeneParts during methylation annotation. #207

Open desmodus1984 opened 11 months ago

desmodus1984 commented 11 months ago

Hi,

I have identified differentially methylated sites with methylKit, and I am interested in annotating the DML/DMR and potentially doing a Gene ontology analysis. I first grabbed all the differentially methylated sites:

DML.ctrl.min<- getMethylDiff(Diff.ctrl.min,
                              difference=-46,
                              qvalue=0.01)

and then, I annotated them with annotateWithGeneParts

DML.ctrl.min.anot <- annotateWithGeneParts(target = as(DML.ctrl.min,"GRanges"), 
                                           feature = refseq_anot)

The refseq_anot is from a bed file with tracks of exons, introns, flanks tracks from the NCBI gff file. It technically, worked well > refseq_anot <- readTranscriptFeatures("Bvos_refseq.bed", remove.unusual=FALSE) Reading the table... Calculating intron coordinates...
Calculating exon coordinates... Calculating TSS coordinates... Calculating promoter coordinates... Outputting the final GRangesList...

But then, when I try the annotation, I got this error message:

DML.ctrl.min.anot <- annotateWithGeneParts(target = as(DML.ctrl.min,"GRanges"),

  • feature = refseq_anot) Warning messages: 1: In .merge_two_Seqinfo_objects(x, y) : Each of the 2 combined objects has sequence levels not in the other:
  • in 'x': NW_022882999.1, NW_022884278.1
  • in 'y': NW_022882923.1, NW_022882925.1, NW_022882926.1, NW_022882928.1, NW_022882929.1, NW_022882931.1, NW_022882932.1, NW_022882933.1, NW_022882934.1, NW_022882935.1, NW_022882937.1, NW_022882939.1, NW_022882940.1, NW_022882941.1, NW_022882942.1, NW_022882943.1, NW_022882944.1, NW_022882945.1, NW_022882946.1, NW_022882947.1, NW_022882948.1, NW_022882949.1, NW_022882950.1, NW_022882951.1, NW_022882953.1, NW_022882955.1, NW_022882956.1, NW_022882957.1, NW_022882958.1, NW_022882959.1, NW_022882960.1, NW_022882961.1, NW_022882962.1, NW_022882964.1, NW_022882965.1, NW_022882966.1, NW_022882969.1, NW_022882972.1, NW_022882974.1, NW_022882976.1, NW_022882977.1, NW_022882981.1, NW_022882982.1, NW_022882983.1, NW_022882985.1, NW_022882986.1, NW_022882987.1, NW_022882989.1, NW_022882990.1, NW_022882991.1, NW_022882992.1, NW_022882993.1, NW_022882994.1, NW_022882995.1, NW_022882996 [... truncated] 2: In .merge_two_Seqinfo_objects(x, y) : Each of the 2 combined objects has sequence levels not in the other:
  • in 'x': NW_022882999.1, NW_022884278.1
  • in 'y': NW_022882923.1, NW_022882925.1, NW_022882926.1, NW_022882928.1, NW_022882929.1, NW_022882931.1, NW_022882932.1, NW_022882933.1, NW_022882934.1, NW_022882935.1, NW_022882937.1, NW_022882939.1, NW_022882940.1, NW_022882941.1, NW_022882942.1, NW_022882943.1, NW_022882944.1, NW_022882945.1, NW_022882946.1, NW_022882947.1, NW_022882948.1, NW_022882949.1, NW_022882950.1, NW_022882951.1, NW_022882953.1, NW_022882955.1, NW_022882956.1, NW_022882957.1, NW_022882958.1, NW_022882959.1, NW_022882960.1, NW_022882961.1, NW_022882962.1, NW_022882964.1, NW_022882965.1, NW_022882966.1, NW_022882969.1, NW_022882972.1, NW_022882974.1, NW_022882976.1, NW_022882977.1, NW_022882981.1, NW_022882982.1, NW_022882983.1, NW_022882985.1, NW_022882986.1, NW_022882987.1, NW_022882989.1, NW_022882990.1, NW_022882991.1, NW_022882992.1, NW_022882993.1, NW_022882994.1, NW_022882995.1, NW_022882996 [... truncated] 3: In .merge_two_Seqinfo_objects(x, y) : Each of the 2 combined objects has sequence levels not in the other:
  • in 'x': NW_022882999.1, NW_022884278.1
  • in 'y': NW_022882923.1, NW_022882925.1, NW_022882926.1, NW_022882928.1, NW_022882929.1, NW_022882931.1, NW_022882932.1, NW_022882933.1, NW_022882934.1, NW_022882935.1, NW_022882937.1, NW_022882939.1, NW_022882940.1, NW_022882941.1, NW_022882942.1, NW_022882943.1, NW_022882944.1, NW_022882945.1, NW_022882946.1, NW_022882947.1, NW_022882948.1, NW_022882949.1, NW_022882950.1, NW_022882951.1, NW_022882953.1, NW_022882955.1, NW_022882956.1, NW_022882957.1, NW_022882958.1, NW_022882959.1, NW_022882960.1, NW_022882961.1, NW_022882962.1, NW_022882964.1, NW_022882965.1, NW_022882966.1, NW_022882969.1, NW_022882972.1, NW_022882974.1, NW_022882976.1, NW_022882977.1, NW_022882981.1, NW_022882982.1, NW_022882983.1, NW_022882985.1, NW_022882986.1, NW_022882987.1, NW_022882989.1, NW_022882990.1, NW_022882991.1, NW_022882992.1, NW_022882993.1, NW_022882994.1, NW_022882995.1, NW_022882996 [... truncated] 4: In .merge_two_Seqinfo_objects(x, y) : Each of the 2 combined objects has sequence levels not in the other:
  • in 'x': NW_022882923.1, NW_022882925.1, NW_022882926.1, NW_022882928.1, NW_022882929.1, NW_022882931.1, NW_022882932.1, NW_022882933.1, NW_022882934.1, NW_022882935.1, NW_022882937.1, NW_022882939.1, NW_022882940.1, NW_022882941.1, NW_022882942.1, NW_022882943.1, NW_022882944.1, NW_022882945.1, NW_022882946.1, NW_022882947.1, NW_022882948.1, NW_022882949.1, NW_022882950.1, NW_022882951.1, NW_022882953.1, NW_022882955.1, NW_022882956.1, NW_022882957.1, NW_022882958.1, NW_022882959.1, NW_022882960.1, NW_022882961.1, NW_022882962.1, NW_022882964.1, NW_022882965.1, NW_022882966.1, NW_022882969.1, NW_022882972.1, NW_022882974.1, NW_022882976.1, NW_022882977.1, NW_022882981.1, NW_022882982.1, NW_022882983.1, NW_022882985.1, NW_022882986.1, NW_022882987.1, NW_022882989.1, NW_022882990.1, NW_022882991.1, NW_022882992.1, NW_022882993.1, NW_022882994.1, NW_022882995.1, NW_022882996.1, NW_022882997.1, NW_022882998.1, NW_0228 [... truncated] 5: In .merge_two_Seqinfo_objects(x, y) : Each of the 2 combined objects has sequence levels not in the other:
  • in 'x': NW_022882923.1, NW_022882925.1, NW_022882926.1, NW_022882928.1, NW_022882929.1, NW_022882931.1, NW_022882932.1, NW_022882933.1, NW_022882934.1, NW_022882935.1, NW_022882937.1, NW_022882939.1, NW_022882940.1, NW_022882941.1, NW_022882942.1, NW_022882943.1, NW_022882944.1, NW_022882945.1, NW_022882946.1, NW_022882947.1, NW_022882948.1, NW_022882949.1, NW_022882950.1, NW_022882951.1, NW_022882953.1, NW_022882955.1, NW_022882956.1, NW_022882957.1, NW_022882958.1, NW_022882959.1, NW_022882960.1, NW_022882961.1, NW_022882962.1, NW_022882964.1, NW_022882965.1, NW_022882966.1, NW_022882969.1, NW_022882972.1, NW_022882974.1, NW_022882976.1, NW_022882977.1, NW_022882981.1, NW_022882982.1, NW_022882983.1, NW_022882985.1, NW_022882986.1, NW_022882987.1, NW_022882989.1, NW_022882990.1, NW_022882991.1, NW_022882992.1, NW_022882993.1, NW_022882994.1, NW_022882995.1, NW_022882996.1, NW_022882997.1, NW_022882998.1, NW_0228 [... truncated] 6: In .merge_two_Seqinfo_objects(x, y) : Each of the 2 combined objects has sequence levels not in the other:
  • in 'x': NW_022882923.1, NW_022882925.1, NW_022882926.1, NW_022882928.1, NW_022882929.1, NW_022882931.1, NW_022882932.1, NW_022882933.1, NW_022882934.1, NW_022882935.1, NW_022882937.1, NW_022882939.1, NW_022882940.1, NW_022882941.1, NW_022882942.1, NW_022882943.1, NW_022882944.1, NW_022882945.1, NW_022882946.1, NW_022882947.1, NW_022882948.1, NW_022882949.1, NW_022882950.1, NW_022882951.1, NW_022882953.1, NW_022882955.1, NW_022882956.1, NW_022882957.1, NW_022882958.1, NW_022882959.1, NW_022882960.1, NW_022882961.1, NW_022882962.1, NW_022882964.1, NW_022882965.1, NW_022882966.1, NW_022882969.1, NW_022882972.1, NW_022882974.1, NW_022882976.1, NW_022882977.1, NW_022882981.1, NW_022882982.1, NW_022882983.1, NW_022882985.1, NW_022882986.1, NW_022882987.1, NW_022882989.1, NW_022882990.1, NW_022882991.1, NW_022882992.1, NW_022882993.1, NW_022882994.1, NW_022882995.1, NW_022882996.1, NW_022882997.1, NW_022882998.1, NW_0228 [... truncated]

I used the same genome for annotation methylation calling. Can I trust the annotation results? Is there a way to fix this error?

Lastly, after annotation, how can I retrieve/find the nearest gene to the DML/DMR? I'd like to do, if possible, a gene set/functional enrichment analysis of the DML/DMR.

Thanks.