How Do I Assign Names To Granges Without It Forcing Elementmetadata

Question

[Jeremy Leipzig]

It seems like the casting routine to assign names to GRanges from GappedAlignments is more natural than the GRanges constructor.

library("GenomicRanges")
feature1 <- GRanges(names="feature1",seqnames="chr1", IRanges(start=1, width=100), strand="*")

featureGA <- GappedAlignments(names="feature2", seqnames = Rle("chr1"), pos = as.integer(25),cigar = "100M", strand = strand("*"))
feature2<-as(feature2,"GRanges")

> feature1
GRanges with 1 range and 1 elementMetadata col:
      seqnames    ranges strand |       names
         <Rle> <IRanges>  <Rle> | <character>
  [1]     chr1  [1, 100]      * |    feature1
  ---
  seqlengths:
   chr1
     NA
> feature2
GRanges with 1 range and 0 elementMetadata cols:
       seqnames    ranges strand
          <Rle> <IRanges>  <Rle>
  feature2     chr1 [25, 124]      *
  ---
  seqlengths:
   chr1
     NA

both<-GRangesList(features=feature1,feature2=feature2)
Error in .Method(..., deparse.level = deparse.level) : 
  number of columns for arg 2 do not match those of first arg

> sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: x86_64-redhat-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=C                 LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] GenomicRanges_1.8.4 IRanges_1.14.2      BiocGenerics_0.2.0 

loaded via a namespace (and not attached):
[1] stats4_2.15.0 tools_2.15.0

Answer 1

[Steve Lianoglou]

Set the names() after the GRanges object is constructed:

feature1 <- GRanges(seqnames="chr1", IRanges(start=1, width=100), strand="*")
names(feature1) <- 'feature1'

featureGA <- GappedAlignments(names="feature2", seqnames = Rle("chr1"), pos = as.integer(25),cigar = "100M", strand = strand("*"))
feature2 <-as(featureGA,"GRanges")

Will almost get you what you want ...

GRangesList(features=feature1,feature2=feature2)
GRangesList of length 2:
$features 
GRanges with 1 range and 0 elementMetadata cols:
           seqnames    ranges strand
              <Rle> <IRanges>  <Rle>
  feature1     chr1  [1, 100]      *

$feature2 
GRanges with 1 range and 0 elementMetadata cols:
           seqnames    ranges strand
  feature2     chr1 [25, 124]      *

---
seqlengths:
 chr1
   NA

... almost