Dear All,
I have installed VariantAnnotation and I am doing the following to locate variants
library(VariantAnnotation)
library(TxDb.Mmusculus.UCSC.mm9.knownGene)
txdb <- TxDb.Mmusculus.UCSC.mm9.knownGene
head(seqlevels(txdb))
peak.file =read.table ("D:\\lena\\TOTAL.peak.target.genes.list.txt", header=T, sep='\t')
pr <- RangedData(IRanges(start=peak.file$start, end=peak.file$end), space=peak.file$chromosome, idx=1:nrow(peak.file))
loc <- locateVariants(pr, txdb, CodingVariants())
and I get the following error....
Error in function (classes, fdef, mtable) :
unable to find an inherited method for function "locateVariants", for signature "RangedData", "TranscriptDb"
Do you have any idea what it means?
I would thought that the installation wasn't ok but when I check into my libraries I can see the varriantannotation library
What should I do?
Thank you
Best regards Lena
•
written
by
e.karasmani •
RangedData is probably not an allowed argument type - it looks like you can use GRanges though. You might be able to cast your RangedData object as a GRanges
pr_GR <- as(pr,"GRanges")
if that doesn't work then just create one from scratch
pr_GR <- GRanges(seqnames=Rle(peak.file$chromosome),ranges=IRanges(start=peak.file$start, end=peak.file$end),strand="*")
thanks for the answer
I tried both the ways and I get the following error
Error in function (classes, fdef, mtable) :
unable to find an inherited method for function "locateVariants", for signature "RangedData", "TranscriptDb"
I don't get what is going on.....
did you remember to use pr_GR instead or pr?
yes I did....
first I did the RangedData and then from that I did the GRange and I receive this error..
what do you think?
paste in your new code
here it is
library(VariantAnnotation)
library(TxDb.Mmusculus.UCSC.mm9.knownGene)
txdb <- TxDb.Mmusculus.UCSC.mm9.knownGene
head(seqlevels(txdb))
peak.file =read.table ("/data/lena/.chip=20.txt", header=T, sep='\t')
pr <- RangedData(IRanges(start=peak.file$start, end=peak.file$end), space=peak.file$chromosome, idx=peak.file$target.gene.name)
pr
pr_GR <- as(pr,"GRanges")
pr_GR <- GRanges(seqnames=Rle(peak.file$chromosome),ranges=IRanges(start=peak.file$start, end=peak.file$end),strand="*")
pr_GR
loc <- locateVariants(pr_GR, txdb, CodingVariants())
and i get the following
Error in function (classes, fdef, mtable) :
unable to find an inherited method for function "locateVariants", for signature "RangedData", "TranscriptDb"
What should I do?
Please help me....
loc <- locateVariants(pr_GR, txdb, CodingVariants())
sorry I made a typo....I had
loc <- locateVariants(pr_GR, txdb, CodingVariants())
that error does not make sense unless you are passing it RangedData. try this code:
library(VariantAnnotation)
library(TxDb.Mmusculus.UCSC.mm9.knownGene)
txdb <- TxDb.Mmusculus.UCSC.mm9.knownGene
pr_GR<-GRanges(seqnames =Rle(c("chr1", "chr1", "chr1", "chr1")),
ranges = IRanges(c(90097186,89700255,183583510,34609177), width = 1),
strand = "*",
refAllele=rep(DNAStringSet("A"),4),
varAllele=rep(DNAStringSet("T"),4))
loc <- locateVariants(pr_GR, txdb, CodingVariants())
this is what I am doing and what I get here it is
library(VariantAnnotation)
library(TxDb.Mmusculus.UCSC.mm9.knownGene)
txdb <- TxDb.Mmusculus.UCSC.mm9.knownGene
head(seqlevels(txdb))
peak.file =read.table ("/data/lena/.chip=20.txt", header=T, sep='\t')
pr <- RangedData(IRanges(start=peak.file$start, end=peak.file$end), space=peak.file$chromosome, idx=peak.file$target.gene.name)
pr
pr_GR <- as(pr,"GRanges")
pr_GR <- GRanges(seqnames=Rle(peak.file$chromosome),ranges=IRanges(start=peak.file$start, end=peak.file$end),strand="*")
pr_GR
Here I get this warning but I don't think it is important
Warning message:
In newGRanges("GRanges", seqnames = seqnames, ranges = ranges, strand = strand, :
missing values in strand converted to "*"
so I am saying
class(pr_GR)
[1] "GRanges"
attr(,"package")
[1] "GenomicRanges"
then I am doing that
loc <- locateVariants(pr_GR, txdb, CodingVariants())
and I get that error
Error in genes[followIdx] :
subscript contains NAs or out of bounds indices
I don't understand what is going on......
Sorry for that....I am a rookie in this field
Do you have any idea?
Thank you in advance
Best regards Lena
show us a sample of your pr_GR: head(pr_GR)
here you are
head (pr_GR)
GRanges with 6 ranges and 0 elementMetadata values:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chr1 [ 9933699, 9934385] *
[2] chr1 [ 88255056, 88257357] *
[3] chr1 [ 88421225, 88425605] *
[4] chr1 [ 95341332, 95342552] *
[5] chr1 [133806728, 133807938] *
[6] chr1 [133903801, 133905113] *
---
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
what do you think?
those work fine. keep taking bigger chunks of your prGR (head(prGR,100)...head(prGR,500)...head(prGR,2000)) until you nail down the culprit.
> pr_GR<-GRanges(seqnames =Rle(c("chr1", "chr1", "chr1", "chr1", "chr1", "chr1")),
+ ranges = IRanges(start=c(9933699,88255056,88421225,95341332,133806728,133903801), end=c(9934385,88257357,88425605,95342552,133807938,133905113)),
+ strand = "*")
> locateVariants(pr_GR, txdb, CodingVariants())
DataFrame with 6 rows and 4 columns
queryHits txID geneID Location
<integer> <character> <CompressedCharacterList> <factor>
1 1 NA 70675,73824 intergenic
2 2 NA 15559,17975 intergenic
3 3 NA 71863,19231 intergenic
4 4 2646 110611 intron
5 5 NA 98415,98415 intergenic
6 6 NA 13714,13714 intergenic
i have made the pr_GR as a data frame and saved it and and I checked.....there are no NAs in the file and it looks ok
here is an example
head(pr_GR,2000)
GRanges with 2000 ranges and 0 elementMetadata values:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chr1 [ 9933699, 9934385] *
[2] chr1 [ 88255056, 88257357] *
[3] chr1 [ 88421225, 88425605] *
[4] chr1 [ 95341332, 95342552] *
[5] chr1 [133806728, 133807938] *
[6] chr1 [133903801, 133905113] *
[7] chr1 [137042981, 137044514] *
[8] chr1 [171447596, 171448584] *
[9] chr1 [172993767, 172997056] *
... ... ... ...
[1992] chr1 [31787477, 31787891] *
[1993] chr1 [32972614, 32973160] *
[1994] chr1 [35847483, 35847803] *
[1995] chr1 [36588633, 36589271] *
[1996] chr1 [37835024, 37835447] *
[1997] chr1 [38238071, 38238419] *
[1998] chr1 [44352200, 44352632] *
[1999] chr1 [44953809, 44954194] *
[2000] chr1 [59402035, 59402338] *
---
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
and
head(pr_GR,500000)
GRanges with 52445 ranges and 0 elementMetadata values:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chr1 [ 9933699, 9934385] *
[2] chr1 [ 88255056, 88257357] *
[3] chr1 [ 88421225, 88425605] *
[4] chr1 [ 95341332, 95342552] *
[5] chr1 [133806728, 133807938] *
[6] chr1 [133903801, 133905113] *
[7] chr1 [137042981, 137044514] *
[8] chr1 [171447596, 171448584] *
[9] chr1 [172993767, 172997056] *
... ... ... ...
[52437] chrY [1664480, 1664889] *
[52438] chrY [ 500256, 500631] *
[52439] chrY [1663851, 1664427] *
[52440] chrY [1398029, 1398387] *
[52441] chrY [ 346885, 347200] *
[52442] chrY [2773727, 2774095] *
[52443] chrY [2853026, 2853651] *
[52444] chrY [2765621, 2765989] *
[52445] chrY [2868909, 2871139] *
---
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
I don't know what should I do.....
You need to actually try these chunks with locateVariants. This is debugging 101.
pr_GR_sample<-head(pr_GR,500000)
locateVariants(pr_GR_sample, txdb, CodingVariants())
Thanks,
I have tried that and here is what I did
pr3=head(pr_GR,52000)
loc2 <- locateVariants(pr3, txdb, AllVariants())
DataFrame with 80324 rows and 4 columns
queryHits txID geneID Location
<integer> <character> <CompressedCharacterList> <factor>
1 1 NA 70675,73824 intergenic
2 2 NA 15559,17975 intergenic
3 3 NA 71863,19231 intergenic
4 4 2646 110611 intron
5 5 NA 98415,98415 intergenic
6 6 NA 13714,13714 intergenic
7 7 NA 320139,68724 intergenic
8 8 3339 66977 intron
9 8 3340 66977 intron
... ... ... ... ...
80316 51996 NA 59026 intron
80317 51996 NA 59026 intron
80318 51996 NA 59026 intron
80319 51996 NA 59026 intron
80320 51996 NA 59026 intron
80321 51997 NA 24061,245666 intergenic
80322 51998 NA 12229 intron
80323 51999 NA 74279,14735 intergenic
80324 52000 NA 78755,78755 intergenic
It doesn't look ok the output
What do you think is going on?
Neither of the columns look like what they supposed to be according to the manual of the Varriant annotation library.... Don't you agree?
Do you have any idea?
Thanks Lena
Hi Lena,
What part of this output looks wrong? It looks ok to me. A variant in an intron region will have a geneID but an intergenic variant (one that falls inbetween genes) will have geneID's for both the preceding and following genes.
Valerie
Hi e.karasmani,
Are you still having problems with this? If yes, please show the first few lines of the GRanges you have created. The error message you are getting implies that the RangedData has not been successfully coerced to a GRanges. You can also confirm this with
class(pr_GR)
Jeremy is correct in that RangedData is not an allowed input. To see all possible inputs use the showMethods() function,
showMethods("locateVariants")
Function: locateVariants (package VariantAnnotation)
query="GRanges", subject="GRangesList", region="CodingVariants"
query="GRanges", subject="GRangesList", region="FiveUTRVariants"
query="GRanges", subject="GRangesList", region="IntergenicVariants"
query="GRanges", subject="GRangesList", region="IntronVariants"
query="GRanges", subject="GRangesList", region="SpliceSiteVariants"
query="GRanges", subject="GRangesList", region="ThreeUTRVariants"
query="GRanges", subject="TranscriptDb", region="AllVariants"
query="GRanges", subject="TranscriptDb", region="CodingVariants"
query="GRanges", subject="TranscriptDb", region="FiveUTRVariants"
query="GRanges", subject="TranscriptDb", region="IntergenicVariants"
query="GRanges", subject="TranscriptDb", region="IntronVariants"
query="GRanges", subject="TranscriptDb", region="SpliceSiteVariants"
query="GRanges", subject="TranscriptDb", region="ThreeUTRVariants"
query="Ranges", subject="GRangesList", region="ANY"
query="Ranges", subject="TranscriptDb", region="ANY"
query="VCF", subject="GRangesList", region="ANY"
query="VCF", subject="TranscriptDb", region="ANY"
Any time you have problems with a function in a Bioconductor package feel free to contact the maintainer with questions - contact emails can be found on the man page for the function. Also a post to the Bioconductor mailing list can be helpful.
http://bioconductor.org/help/mailing-list/
Valerie
I am not familiar with this tool. But snpEff is another tool that you can use in case you couldn't resolve this problem.
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