Visualisation of ChIP-seq data in r - function errors in Gviz and biomaRt

Question

[H.Chloe]

Dear all,
I am trying to visualize my chip-seq data in r.
I followed the whole process according to "ChIP-seq analysis basics(Aleksandra P ekowska, Simon Anders)" and there were some problems using BiomartGeneRegionTrack function.

Here is the code I'm using.

library(BSgenome)
library(BSgenome.Dmelanogaster.UCSC.dm6)
library(cluster.datasets)
genome <- BSgenome.Dmelanogaster.UCSC.dm6
si = seqinfo(genome)
si[c("chr2L", "chr2R")]

I tried to visualize a region on the D.melanogaster chromosome(genome dm6) so I changed some code for my data.

library(ShortRead)
library(Gviz) 
library(biomaRt)

fm = Gviz:::.getBMFeatureMap()
fm["symbol"] = "external_gene_id"
bm = BiomartGeneRegionTrack(chromosome = "chr2L", genome = "dm6",
                       start = 1009600, end = 1016000,
                       filter = list("with_ox_refseq_mrna"=T), 
                       size = 4, name = "RefSeq", utr5 = "red3", utr3 = "red3",
                       protein_coding = "black", col.line = NULL, cex = 7, 
                       featureMap = fm)

Error in .getBiomart(genome) : 
Gviz thinks that the UCSC genome identifier 'dm6' should map to the current Biomart head as 'BDGP6', but   its current version is 'BDGP6.22'. Please manually provide biomaRt object

This "BiomartGeneRegionTrack" has some problems, but I don't know why.(I changed wrong word. Thanks!) If anyone knows how to solve this problem, please help me.

Thanks in advance!

Answer 1

[bernatgel]

Your command has a typo! it should be "chromosome" and it's "chrmosome" (missing first o) so it thinks you have specified no chromosome at all.

[bernatgel]

You can also give a try to karyoploteR. It's also an R/Bioconductor package with a different approach to plotting data along the genome. And it can work with any genome, including "dm6".

There's a karyoploteR tutorial with plenty of information and examples, including one on plotting ChIP-seq data and genes using R and karyoploteR to create images like this. Maybe it can help you with your ChIP-seq data!

[H.Chloe]

Thanks for your comment! I changed the spelling for this code! Still there is a problem, I will add it to this post!