Question: Error in RnBeads when customizing promoters
1
gravatar for sugus
18 months ago by
sugus30
China Pharmaceutical University
sugus30 wrote:

Hi there, I got trouble in customizing promoters in RnBeads.
I use the attached promoters2kb.R to customize a defined promoters with + - 2000kb from TSS, and set it to RnBeads.

library(RnBeads)

genome.assembly <- "hg19"   # targeted genome assembly
promoter.upstream <- 2000L  # number of bases upstream of TSS belonging to the promoter
promoter.downstream <- 1999L # number of bases downstream of TSS belonging to the promoter

genes <- rnb.get.annotation("genes", genome.assembly)
genes <- rnb.annotation2data.frame(genes)
pr.start <- ifelse(genes$Strand == "-", genes$End - promoter.downstream, genes$Start - promoter.upstream)
pr.end <- ifelse(genes$Strand == "-", genes$End + promoter.upstream, genes$Start + promoter.downstream)
tbl <- data.frame(
  "chromosome" = genes$Chromosome,
  "start" = pr.start,
  "end" = pr.end,
  "strand" = genes$Strand)
rownames(tbl) <- genes$ID

rnb.set.annotation("promoters2kb", tbl, assembly = genome.assembly)
rnb.options(region.types = c(rnb.getOption("region.types"), "promoters2kb"))

When I command the following code it seemed perfect to me:

head(rnb.get.annotation("promoters2kb"))
GRangesList object of length 6:
$chr1 
GRanges object with 5363 ranges and 0 metadata columns:
                  seqnames                 ranges strand
                     <Rle>              <IRanges>  <Rle>
  ENSG00000223972     chr1         [ 9869, 13868]      +
  ENSG00000243485     chr1         [27554, 31553]      +
  ENSG00000227232     chr1         [27807, 31806]      -
  ENSG00000237613     chr1         [34082, 38081]      -
  ENSG00000268020     chr1         [50473, 54472]      +
              ...      ...                    ...    ...
  ENSG00000171163     chr1 [249151344, 249155343]      -
  ENSG00000227237     chr1 [249151363, 249155362]      +
  ENSG00000185220     chr1 [249198395, 249202394]      +
  ENSG00000200495     chr1 [249204995, 249208994]      -
  ENSG00000233084     chr1 [249228780, 249232779]      +

...
<5 more elements>
-------
seqinfo: 24 sequences from hg19 genome; no seqlengths

and it also appeared in the rnb.region.types when I command rnb.region.types:

> rnb.region.types()
[1] "tiling"        "genes"         "promoters"     "cpgislands"    "promoters2kb"

However, when I use rnb.options and rnb.run.analysis, I got the following warning and of course there is no results coming out.

2017-12-20 16:29:56     1.8 WARNING                                 The following 1 region types will not be included in the analysis: promoters2kb

Also I cannot use M=meth(rnb.set,"promoters2kb") to get beta value, it will return:

M=meth(rnb.set.load,"promoters_2kb")
Error in get.dataset.matrix(object, type, row.names, object@meth.sites,  : 
  unsupported region type

Thus, no idea about what happened and what to figure it out. Somebody help, many thanks in advance!

rnbeads promoters R • 521 views
ADD COMMENTlink written 18 months ago by sugus30

Hi sugus,

By any chance, did you find a solution for your problem? I am facing the same issues.

ADD REPLYlink written 16 months ago by genomix0
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