How to convert 0 based genomic ranges found in CEEHRC bedgraph files into 1 based genomic ranges used in R?
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@helimelanie-15780
Last seen 4.6 years ago

​Hi,

I am using WGBS methylation data from CEEHRC project through DeppBlueR package and visualise it using Gviz. First track is a HM450 probes. Second track is obviously the bases sequence of the genome. Third track is WGBS . 

When plotting these data at high resolution I can see that the methylation data are 1 base left of where it should be (aligned with GC instead of the following CG), as I understand the data and as I can see in UCSC genome browser:

 

I guess that this is because bedgraph data uses 0 based genomic coordinates while R uses 1 based ranges. 

Can I convert CEEHRC 0 based into 1 based coordinates easily so the data align properly to the genome?

Thanks

Mel

PS: I also know that my HM450 probe should also align with only one base... work in progress...  

 

 

library(Gviz)
library(DeepBlueR)
library(FDb.InfiniumMethylation.hg19)
library(BSgenome.Hsapiens.UCSC.hg19)

# HM450 methylation assay probes from FDb.InfiniumMethylation.hg19 package
hm450 <- get450k() 
probenames <- "cg23699648"
probes <- hm450[probenames]
HM450 <- AnnotationTrack(probes,
                         chromosome = "chr6", genome = "hg19", name = "HM450",
                         strand = c("*"),
                         id = 1, cex.title = 0.5, min.width = 2, fill = "darkblue", col = NULL, rotation.title = 0, 
                         fontcolor.feature = "darkblue", background.title="darkgrey")

# WGBS (Methylation) for Breast Luminal progenitors from CEEHRC project track with DeepBlueR package
query_id <- deepblue_select_experiments(
  experiment_name= c("A34409.3_lanes_dupsFlagged.q5.f0.5mC.CpG.fractional.bedgraph"),
  chromosome="chr6", 
  start=121756532, 
  end=121756593
)
request_id <- deepblue_get_regions(query_id=query_id, 
                                   output_format="CHROMOSOME,START,END,VALUE,@BIOSOURCE,@SAMPLE_ID,@NAME,@PROJECT")
regions <-  deepblue_download_request_data(request_id=request_id)
genome(regions) <- "hg19"
regions@elementMetadata[["@CELL_TYPE"]] <-  t(samples[match(regions@elementMetadata[,"@SAMPLE_ID"], samples[[1]]),"cell_type"])
df <- data.frame(iranges = regions)
MethylationProg <- DataTrack(regions, name = "Prog", 
                             genome="hg19", type = "h",  ylim = c(0,100), background.title = "darkgray", cex.title = 0.5, cex.axis = 0.5, col = "#c49d60", lwd.title = 1)

# strack from BSgenome.Hsapiens.UCSC.hg19 package
strack <- SequenceTrack(Hsapiens, chromosome = "chr6", cex = 0.5)

# Plot the track with Gviz package
plotTracks(list(HM450, strack, MethylationProg),
           from = 121756532, to = 121756593, 
           main = "Probe 3", cex.main = 0.9)

 

 

deepbluer gziv • 541 views
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Hi Melanie,

A workaround could be to use the shift function of IRanges, i.e. shift(regions, 1)

Does this help? In any case it would be nice if you could add a bug report to our github page: https://github.com/MPIIComputationalEpigenetics/DeepBlueR/issues 

Best,

Markus

 

 

 

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Entering edit mode

Hi,

Thanks, for the easy workaround! 

I reported the bug. Here it is:

https://github.com/MPIIComputationalEpigenetics/DeepBlueR/issues/46

Thanks again

Mel

 

 

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