Entering edit mode
Dear all,
biocLite(?UniProt.ws?)
libraryUniProt.ws)
selectUniProt.ws,keys=("P02794"),columns=c("DOMAINS","FEATURES"),key
type="UNIPROTKB")
Getting extra data for P02794 NA NA etc
UNIPROTKB DOMAINS
1 P02794 Ferritin-like diiron domain (1)
FEATURES
1 Chain (2); Domain (1); Erroneous initiation (1); Helix (6);
Initiator methionine (1); Metal binding (6); Modified residue (4);
Sequence conflict (1); Turn (2)
What I want are the positional details for each of these features ?
which are visible through the uniprot web page.
FTH1 is 183 amino acids in length. There are 6 metal binding sites,
each at a specific position.
This information is there since you can have the web site return the
positional details. I would like them so I may manipulate them with
new evidential information.
Ultimately I wish to display them with tracks from ggbio ?
pb.53A.pos.ga <- readGAlignmentsFromBam(pb.53A.pos.bamfile,
param = ScanBamParam(which =
genesymbol["FTH1"],what=c("seq")),
use.names = TRUE)
FTH1.ga <- geom_alignment(data = txdb,which=genesymbol["FTH1"])
So here I have sample information which I have aligned to the
reference genome. I retrieve that information from a bam file.
# create the GAlignments objects for each isoform
FTH1.isoform.1 <- pb.53A.pos.ga[c(7)]
FTH1.isoform.2 <- pb.53A.pos.ga[c(15)]
FTH1.isoform.3 <- pb.53A.pos.ga[c(13)]
FTH1.isoform.4 <- pb.53A.pos.ga[c(8)]
FTH1.isoform.5 <- pb.53A.pos.ga[c(2)]
FTH1.isoform.6 <- pb.53A.pos.ga[c(1)]
p1 <- autoplot(FTH1.isoform.1, fill = "brown", color = "brown")
p2 <- autoplot(FTH1.isoform.2, fill = "blue", color = "blue")
p3 <- autoplot(FTH1.isoform.3, fill = "brown", color = "brown")
p4 <- autoplot(FTH1.isoform.4, fill = "brown", color = "brown")
p5 <- autoplot(FTH1.isoform.5, fill = "brown", color = "brown")
p6 <- autoplot(FTH1.isoform.6, fill = "brown", color = "brown")
tracks( FTH1=p1.FTH1,
"Iso 1"=p1,
"Iso 2"=p2,
"Iso 3"=p3,
"Iso 4"=p4,
"Iso 5"=p5,
"Iso 6"=p6)
I then can autopilot each of the separate isoforms. What I want to
do however, is annotate the isoforms so that they each show the coding
region with the full height of the bar, and a reduced height for the
non-coding regions.
Additionally, I want to color the graphic with the details for the
protein, such as the metal binding sites, domains, etc. So that
computationally I can generate an informative picture which explains
what is lost or gained in separate isoforms.
Thoughts?
Anne
R version 3.1.0 (2014-04-10)
Platform: x86_64-apple-darwin13.1.0 (64-bit)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] parallel stats graphics grDevices utils datasets
methods
[8] base
other attached packages:
[1] UniProt.ws_2.4.2
[2] RCurl_1.95-4.3
[3] bitops_1.0-6
[4] RSQLite_0.11.4
[5] DBI_0.2-7
[6] biomaRt_2.20.0
[7] BiocInstaller_1.14.2
[8] GenomicAlignments_1.0.5
[9] BSgenome_1.32.0
[10] Rsamtools_1.16.1
[11] Biostrings_2.32.1
[12] XVector_0.4.0
[13] ggbio_1.12.8
[14] ggplot2_1.0.0
[15] TxDb.Hsapiens.UCSC.hg19.knownGene_2.14.0
[16] GenomicFeatures_1.16.2
[17] AnnotationDbi_1.26.0
[18] Biobase_2.24.0
[19] GenomicRanges_1.16.4
[20] GenomeInfoDb_1.0.2
[21] IRanges_1.22.10
[22] BiocGenerics_0.10.0
loaded via a namespace (and not attached):
[1] BatchJobs_1.3 BBmisc_1.7
BiocParallel_0.6.1
[4] biovizBase_1.12.1 brew_1.0-6 checkmate_1.2
[7] cluster_1.15.2 codetools_0.2-8
colorspace_1.2-4
[10] dichromat_2.0-0 digest_0.6.4 fail_1.2
[13] foreach_1.4.2 Formula_1.1-2 grid_3.1.0
[16] gridExtra_0.9.1 gtable_0.1.2 Hmisc_3.14-4
[19] iterators_1.0.7 labeling_0.2 lattice_0.20-29
[22] latticeExtra_0.6-26 MASS_7.3-33 munsell_0.4.2
[25] plyr_1.8.1 proto_0.3-10
RColorBrewer_1.0-5
[28] Rcpp_0.11.2 reshape2_1.4
rtracklayer_1.24.2
[31] scales_0.2.4 sendmailR_1.1-2 splines_3.1.0
[34] stats4_3.1.0 stringr_0.6.2 survival_2.37-7
[37] tcltk_3.1.0 tools_3.1.0
VariantAnnotation_1.10.5
[40] XML_3.98-1.1 zlibbioc_1.10.0
[[alternative HTML version deleted]]
