I have used the code in another question https://support.bioconductor.org/p/67118/#97616,but it didn't work with me, I have those Segment_Mean, a start and end I want to know which genes overlap with those regions.
xx = splitColumnByOverlap(gns, cnv, "SYMBOL")
Warning message:
In .Seqinfo.mergexy(x, y) :
The 2 combined objects have no sequence levels in common. (Use
suppressWarnings() to suppress this warning.)
my cnv is the copy number variation file for tumor tissue only
GRanges object with 284458 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] 1 [ 3218610, 95674710] *
[2] 1 [ 95676511, 95676518] *
[3] 1 [ 95680124, 167057183] *
[4] 1 [167057495, 167059336] *
[5] 1 [167059760, 181602002] *
... ... ... ...
[284454] 19 [ 284018, 58878226] *
[284455] 20 [ 455764, 62219837] *
[284456] 21 [15347621, 47678774] *
[284457] 22 [17423930, 49331012] *
[284458] 23 [ 3157107, 154905589] *
-------
seqinfo: 23 sequences from an unspecified genome; no seqlengths
my data file look like the following(part of it)
Sample | Chromosome | Start | End | Num_Probes | Segment_Mean |
TCGA-3C-AAAU-01A-11D-A41E-01 | 1 | 3218610 | 63469503 | 33369 | 0.1791 |
TCGA-3C-AAAU-01A-11D-A41E-01 | 1 | 63471492 | 63472103 | 3 | -0.8257 |
TCGA-3C-AAAU-01A-11D-A41E-01 | 1 | 63472868 | 85632596 | 13663 | 0.2994 |
TCGA-3C-AAAU-01A-11D-A41E-01 | 1 | 85635413 | 85878136 | 146 | 0.6498 |
TCGA-3C-AAAU-01A-11D-A41E-01 | 1 | 85881278 | 149890533 | 20618 | 0.2781 |
@Vincent J. Carey, Jr.
I had the following error too
subsetByOverlaps(genes(EnsDb.Hsapiens.v75), mygr)
Error in genes(EnsDb.Hsapiens.v75) :
object 'EnsDb.Hsapiens.v75' not found
in addition to I have tried the code and I used the r2syms as you wrote then
> mygr = GRanges(ss$Chromosome, IRanges(ss$Start, ss$End))
> fo = findOverlaps(mygr, r2syms)
Warning message:
In .Seqinfo.mergexy(x, y) :
The 2 combined objects have no sequence levels in common. (Use
suppressWarnings() to suppress this warning.)
what should I do?