library("Pbase")
f0 <- "~/Data2/Thermo_HELA_PRT/swissprot_human_canonical_19_09_12.fasta"
p0 <- Proteins(f0)
p1 <- addIdentificationData(p0, "~/Data2/Thermo_HELA_PRT/Thermo_Hela_PRTC_1.mzid",
TRUE)
p2 <- addIdentificationData(p0, "~/Data2/Thermo_HELA_PRT/Thermo_Hela_PRTC_1.mzid",
FALSE)
## only 10 proteins, chosen as follows
## lns <- elementNROWS(pranges(p0))
## plns <- elementNROWS(aa(p0))
## i <- which(lns > 20)
## j <- which(lns < 6 & lns > 3)
## c(i[1:5], j[1:5])
f <- "./swissprot_human_canonical_10.fasta"
p <- Proteins(f)
p <- addIdentificationData(p, "~/Data2/Thermo_HELA_PRT/Thermo_Hela_PRTC_1.mzid")
save(p, file = "../data/p.rda")
plot(p)
## at <- ATrack(start = c(250, 480), end = c(320, 520),
## name = "Annotations")
## pat1 <- ProteinAxisTrack()
## pat2 <- ProteinAxisTrack()
## plotTracks(pat, from = 1, to = 850)
## pat <- ProteinAxisTrack(addNC = TRUE, littleTicks = TRUE)
## seqEx <- aa(p)[[1]]
## plotTracks(trackList = c(pat, st), from = 1, to = 40)
## pat<-ProteinAxisTrack(addNC = TRUE, littleTicks = TRUE)
## data(pep_hxb2)
## hxb2_seq <- metadata(pep_hxb2)$sequence
## st <- ProteinSequenceTrack(sequence = hxb2_seq, name = "env")
## s2 <- paste(strsplit(hxb2_seq, "")[[1]][1:100], collapse = "")
## st2 <- ProteinSequenceTrack(sequence = s2, name = "s2")
## plotTracks(trackList = c(pat, st, st2), from = 1, to = 500)
## png("p1.png")
## plotTracks(trackList = c(pat, st, st2), from = 1, to = 200)
## dev.off()
## png("p2.png")
## plotTracks(trackList = c(pat, st, st2), from = 1, to = 1000)
## dev.off()
library("pRoloc")
## load("~/ResearchProjects/collaborations/fusion-data-analysis/data/pdRes-2014-03-22.rda", verbose = TRUE)
load("~/ResearchProjects/collaborations/fusion-data-analysis/data/svmRes-2014-04-15-top.25.rda", verbose=TRUE)
setStockcol(NULL)
setStockcol(paste0(getStockcol(), "80"))
ptsze <- exp(fData(svmRes.2014.03.27)$svm.scores) - 1
pdf("../Figures/fus.pdf")
plot2D(svmRes.2014.03.27, fcol = "svm")
addLegend(svmRes.2014.03.27, fcol = "svm",
where = "bottomleft", bty = "n",
cex = .8)
dev.off()
########################################
library("biomaRt")
## Accession: P53501
## Name: ACT3_DROME
## FBgn0000044
## P60709 (ACTB_HUMAN)
## ENSG00000075624
ens <- useMart("ensembl", "dmelanogaster_gene_ensembl")
select(ens, keys = "P53501",
keytype = "uniprot_swissprot",
columns = c(columns(ens)[1:12],
"uniprot_swissprot"))
select(ens, keys = "ACT3_DROME",
keytype = "uniprot_swissprot",
columns = c(columns(ens)[1:12],
"uniprot_swissprot"))
ens <- useMart("ensembl", "hsapiens_gene_ensembl")
select(ens, keys = "P60709",
keytype = "uniprot_swissprot",
columns = c(columns(ens)[1:12],
"uniprot_swissprot"))
select(ens, keys = "ACTB_HUMAN",
keytype = "uniprot_swissprot",
columns = c(columns(ens)[1:12],
"uniprot_swissprot"))
ens <- useMart("ensembl", "mmusculus_gene_ensembl")
bm <- select(ens, keys = "DTX4_MOUSE",
keytype = "uniprot_swissprot",
columns = c("ensembl_exon_id",
"peptide",
"exon_chrom_start",
"exon_chrom_end"))
bm <- select(ens, keys = "DTX4_MOUSE",
keytype = "uniprot_swissprot",
columns = c(
"ensembl_gene_id",
"ensembl_transcript_id",
"ensembl_peptide_id",
"ensembl_exon_id",
"description",
"chromosome_name",
"strand",
"exon_chrom_start",
"exon_chrom_end",
"5_utr_start",
"5_utr_end",
"3_utr_start",
"3_utr_end",
"start_position",
"end_position"))
## "band",
## "transcript_start",
## "transcript_end",
## "exon_chrom_start",
## "exon_chrom_end",
## "rank",
## "uniprot_swissprot",
## "uniprot_swissprot",
## "gene_exon",
## "cdna",
## "coding",
## "peptide"))
library("AnnotationHub")
hub <- AnnotationHub()
## data exploration
length(names(hub)) ## resources available
md <- metadata(hub) ## DataFrame
dna <- hub$ensembl.release.74.fasta.mus_musculus.dna.Mus_musculus.GRCm38.74.dna.toplevel.fa.rz
## dnax <- readDNAStringSet(dna$index)
pep <- hub$ensembl.release.74.fasta.mus_musculus.pep.Mus_musculus.GRCm38.74.pep.all.fa.rz
gtf <- hub$ensembl.release.74.gtf.mus_musculus.Mus_musculus.GRCm38.74.gtf_0.0.1.RData
i <- which(gtf$protein_id == "ENSMUSP00000040229")
gtf[i]
library("Gviz")
library("BSgenome")
library("BSgenome.Mmusculus.UCSC.mm10")
mus <- Mmusculus
## getSeq(mus, gtf[i])
library(TxDb.Mmusculus.UCSC.mm10.knownGene)
xdb <- TxDb.Mmusculus.UCSC.mm10.knownGene
##txdb <- extractTranscriptSeqs(mus, TxDb.Mmusculus.UCSC.mm10.knownGene)
####################
ens <- useMart("ensembl", "mmusculus_gene_ensembl")
## was not mapped by Alejandro
bm <- select(ens, keys = "SARNP_MOUSE",
keytype = "uniprot_swissprot",
columns = c(
"ensembl_gene_id",
"ensembl_transcript_id",
"ensembl_peptide_id",
"ensembl_exon_id",
"description",
"chromosome_name",
"strand",
"exon_chrom_start",
"exon_chrom_end",
"5_utr_start",
"5_utr_end",
"3_utr_start",
"3_utr_end",
"start_position",
"end_position"))
###################################
library("BSgenome.Hsapiens.UCSC.hg19")
library("TxDb.Hsapiens.UCSC.hg19.knownGene")
txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
tx_seqs <- extractTranscriptSeqs(BSgenome.Hsapiens.UCSC.hg19, txdb)
tr <- transcripts(txdb)
(cds <- cdsBy(txdb))
cds_seqs <- extractTranscriptSeqs(BSgenome.Hsapiens.UCSC.hg19, cds)
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