Entering edit mode
Hi Martin,
I'd really like to help, but from you code below I can't tell for
which genome you are trying to do this (the value of 'gen'). I also
have no idea how you came up with the 'track.name' vector.
In general, Gviz is using rtracklayer::tableNames to figure out which
tables and tracks are available. So you should get the same results,
assuming that you checked for the same chromosome.
Also please always include the output of sessionInfo() when asking for
help in order for us to know which R and package version we are
dealing with.
Florian
From: <martin>, Tiphaine
<tiphaine.martin@kcl.ac.uk<mailto:tiphaine.martin@kcl.ac.uk>>
Date: Thursday, February 13, 2014 11:18 PM
To: Florian Hahne
<florian.hahne@novartis.com<mailto:florian.hahne@novartis.com>>
Subject: Gviz problem to extract some track with UcscTrack like Broad
ChromHMM
Dear Florian,
I am trying to use your package Gviz to visualise my data and some
data from UCSC, for example: "Broad ChromHMM. But I have a error
message.
I dont understand because I have checked with the package
rtracklayer, whose your package inherits, the name of tracks and
tables. Could you help me ?
Regards
Tiph
R Command used to find the name of track and table
>track.names["Broad ChromHMM"]
Broad ChromHMM
wgEncodeBroadHmm"
>sapply(track, function(track) {
+ tableNames(ucscTableQuery(mySession, track=track))
+ })
Broad ChromHMM
[1,] "wgEncodeBroadHmmGm12878HMM"
[2,] "wgEncodeBroadHmmH1hescHMM"
[3,] "wgEncodeBroadHmmK562HMM"
[4,] "wgEncodeBroadHmmHepg2HMM"
[5,] "wgEncodeBroadHmmHuvecHMM"
[6,] "wgEncodeBroadHmmHmecHMM"
[7,] "wgEncodeBroadHmmHsmmHMM"
[8,] "wgEncodeBroadHmmNhekHMM"
[9,] "wgEncodeBroadHmmNhlfHMM"
> UcscTrack(genome = gen, chrom
My errors when I try to use UcscTrack:
> UcscTrack(genome = gen, chromosome = chr, track = "Broad ChromHMM",
+ table="wgEncodeBroadHmmGm12878HMM",
+ from = start, to = end, trackType = "AnnotationTrack",
+ rstarts = "chromStart", rends = "chromEnd", gene = "name",
+ symbol = "name", strand = "strand",
+ fill = "itemRgb", name = "UCSC Genes)
Error in match.arg(track, sort(c(availTracks, names(availTracks)))) :
'arg' should be one of 1000G Ph1 Accsbl, 1000G Ph1 Vars, 46-Way
Cons, 5% Lowest S, acembly, AceView Genes, Affy Exon Array,
Affy GNF1H, Affy RNA Loc, Affy U133, Affy U133Plus2, Affy
U95, affyExonArray, affyGnf1h, affyU133, affyU133Plus2,
affyU95, All SNPs(132), All SNPs(135), All SNPs(137), All
SNPs(138), Allen Brain, allenBrainAli, allHg19RS_BW,
altSeqComposite10, Assembly, BAC End Pairs, bacEndPairs, Base
Position, BU ORChID, Burge RNA-seq, burgeRnaSeqGemMapperAlign,
CCDS, ccdsGene, CD34 DnaseI, CGAP SAGE, cgapSage,
chainSelf, Chromosome Band, clinvar, ClinVar Variants, Common
SNPs(132), Common SNPs(135), Common SNPs(137), Common
SNPs(138), Cons Indels MmCf, cons100way, cons46way, Conserv
> UcscTrack(genome = gen, chromosome = chr, track =
"wgEncodeBroadHmm",
+ table="wgEncodeBroadHmmGm12878HMM",
+ from = start, to = end, trackType = "AnnotationTrack",
+ rstarts = "chromStart", rends = "chromEnd", gene = "name",
+ symbol = "name", strand = "strand",
+ fill = "itemRgb", name = "UCSC Genes)
Error in match.arg(track, sort(c(availTracks, names(availTracks)))) :
'arg' should be one of 1000G Ph1 Accsbl, 1000G Ph1 Vars, 46-Way
Cons, 5% Lowest S, acembly, AceView Genes, Affy Exon Array,
Affy GNF1H, Affy RNA Loc, Affy U133, Affy U133Plus2, Affy
U95, affyExonArray, affyGnf1h, affyU133, affyU133Plus2,
affyU95, All SNPs(132), All SNPs(135), All SNPs(137), All
SNPs(138), Allen Brain, allenBrainAli, allHg19RS_BW,
altSeqComposite10, Assembly, BAC End Pairs, bacEndPairs, Base
Position, BU ORChID, Burge RNA-seq, burgeRnaSeqGemMapperAlign,
CCDS, ccdsGene, CD34 DnaseI, CGAP SAGE, cgapSage,
chainSelf, Chromosome Band, clinvar, ClinVar Variants, Common
SNPs(132), Common SNPs(135), Common SNPs(137), Common
SNPs(138), Cons Indels MmCf, cons100way, cons46way, Conserv
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