YuLab-SMU
Some problem about Chipseeker 1.44
Dear Professor
Hello, I have two questions. Question 1: I have output the result, and I used SameSrand=TRUE, which mostly works. My bed file is full of positive chains, but there are a few positive chains annotated to the promoter of the negative chain gene. Why is this? I used SameSrand=TRUE, However, there are still some positive chain coordinates annotated to the negative chain gene promoter, simply because the positive chain coordinates are relatively close to the negative chain promoter.What should I do? Question 2: I have a total of 850k coordinates, all of which are positive chains, but I have annotated 800k. How can the remaining 50k be displayed? Please help me, thank you.
annotatePeak( peak, tssRegion = c(-2000, 100), TxDb = txdb, level = "transcript", assignGenomicAnnotation = TRUE, genomicAnnotationPriority = c("Promoter", "5UTR", "3UTR", "Exon", "Intron", "Downstream", "Intergenic"), annoDb = "org.Dr.eg.db", addFlankGeneInfo = FALSE, flankDistance = 5000, sameStrand = TRUE, ignoreOverlap = FALSE, ignoreUpstream = FALSE, ignoreDownstream = FALSE, overlap = "all", verbose = TRUE, columns = c("ENTREZID", "ENSEMBL", "SYMBOL", "GENENAME") )
done... Annotated peaks generated by ChIPseeker 822538/858148 peaks were annotated Genomic Annotation Summary:
