Hello,

I am not able to change seqlevels (as I think I was used to) for GRanges objects.

seqlevels (gr) <- seqlevels (noexons1)
Fehler in getDanglingSeqlevels(x, new2old = new2old, force = force, seqlevels(value)): won't drop seqlevels currently in use (ch8), unless you use 'force=TRUE' to also drop elements in 'x' where those seqlevels are used
(e.g. with 'seqlevels(x, force=TRUE) <- new_seqlevels').
Alternatively, you can also subset 'x' first.

Trying ...

seqlevels (gr, force=TRUE) <- seqlevels (noexons1)

... leaves my with a granges object without ranges :

gr
GRanges with 0 ranges and 1 metadata column:
   seqnames    ranges strand |       NIC
      <Rle> <IRanges>  <Rle> | <numeric>
  ---
  seqlengths:
    chr1 chr10 chr11 chr12 chr13 chr14 ...  chr6  chr7  chr8  chr9  chrX  chrY
      NA    NA    NA    NA    NA    NA ...    NA    NA    NA    NA    NA    NA

However, after the following procedure it works ...

seqlevels (gr) <- "chr8"
seqlevels (gr) <- seqlevels (noexons1)

Can anybody explain this behaviour? What is the "normal" syntax to change seqlevels?

Thanks

Hermann
 

dput (gr)
new("GRanges"
    , seqnames = new("Rle"
    , values = structure(1L, .Label = "ch8", class = "factor")
    , lengths = 4L
    , elementMetadata = NULL
    , metadata = list()
)
    , ranges = new("IRanges"
    , start = c(25951L, 91936L, 139793L, 155757L)
    , width = c(1L, 1L, 1L, 1L)
    , NAMES = NULL
    , elementType = "integer"
    , elementMetadata = NULL
    , metadata = list()
)
    , strand = new("Rle"
    , values = structure(3L, .Label = c("+", "-", "*"), class = "factor")
    , lengths = 4L
    , elementMetadata = NULL
    , metadata = list()
)
    , elementMetadata = new("DataFrame"
    , rownames = NULL
    , nrows = 4L
    , listData = structure(list(NIC = c(0.304211024770134, 0.700993422278323,
0.528789378129407, 0.528789378129407)), .Names = "NIC")
    , elementType = "ANY"
    , elementMetadata = NULL
    , metadata = list()
)
    , seqinfo = new("Seqinfo"
    , seqnames = "ch8"
    , seqlengths = NA_integer_
    , is_circular = NA
    , genome = NA_character_
)
    , metadata = list()
)
 seqlevels (noexons1)
[1] "chr1"  "chr10" "chr11" "chr12" "chr13" "chr14" "chr15" "chr16" "chr17"
[10] "chr18" "chr19" "chr2"  "chr20" "chr21" "chr22" "chr3"  "chr4"  "chr5"
[19] "chr6"  "chr7"  "chr8"  "chr9"  "chrX"  "chrY"

Does this help?

> seqlevelsStyle(gr)
[1] "dbSNP"
> seqlevelsStyle(gr) <- "UCSC"
> seqlevels(gr)
[1] "chr8"

In other words, you have dbSNP seqlevels currently, and you are trying to convert to UCSC style seqlevels AND add the other chromosomes in one step. Since ch8 != chr8, you lose all seqlevels.

Hm ...

Yes, it helps ... Actually it was a typo 'ch8' instead of 'chr8'. Many thanks.