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!