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:
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")
)