search for: peptides

...) result <- new('S4_result_class') result@proteins <- xpathApply(xml.doc, "//model/protein", function(protein.node) { protein <- new('S4_protein_class') ## fill in a couple of attributes of the protein object using xmlValue and xmlAttrs(protein.node) protein@peptides <- xpathApply(protein.node, "./peptide", function(peptide.node) { peptide <- new('S4_peptide_class') ## fill in a couple of attributes of the peptide object using xmlValue and xmlAttrs(peptide.node) peptide@aas <- sapply(xmlElementsByTagName(peptide.node, name...

...ved?). ? to access to the ith peptide, you can use X$Peptide[i] ? to access to the ith label, you can use X$Label[i] define a set of amino acids using string or other format if you want amino.acid<-"ACDEFGHIKLMNPQRSTVWY" define two matrices with initialised entries, one for cleaved peptides and one for none-cleaved peptides ? matrix(0,AA,mer),where AA is the number of amino acids, and mer is the number of residues detected from data using the nchar function ? both matrices have the same size, the number of rows being equal to the number of amino acids and the number of columns being e...

Dear all, Attached is a description of my data, graph and the problem which I need help with. Hope you have time to open the file and help me out. Many thanks, Jenny ---------------------------------

...options="XML"> <protein_group group_number="1" probability="1.0000"> <protein protein_name="sp|P00004|CYC_HORSE" n_indistinguishable_proteins="1" probability="1.0000" percent_coverage="46.7" unique_stripped_peptides="EDLIAYLK+EETLMEYLENPK +KTGQAPGFTYTDANK+TEREDLIAYLK+TGPNLHGLFGR+TGQAPGFTYTDANK" group_sibling_id="a" total_number_peptides="226" pct_spectrum_ids="2.54" confidence="1.00"> <parameter name="prot_length" value="107&...

Hi !  Facing problem with " getSequence" commend .  when only biomaRt package loaded the following example working well  >mart <- useMart("ensembl",dataset="hsapiens_gene_ensembl") >seq = getSequence(id="BRCA1", type="hgnc_symbol", seqType="peptide", mart = mart) show(seq) but when i have loaded the seqinr, i got problem

I have following codes for ggplots. The legends are given in the plot do not match with the values specified in the codes given below. Your helps highly appreciated. Greg library(ggplot2) p <- ggplot(a,aes(x=NO_BMI_FI_beta ,y=FI_beta ,color= Super.Pathway))+ theme_bw() +theme(panel.border=element_blank()) + geom_point(size=3) p2<-p+scale_color_manual(name="Super.Pathway",

Hi I am attempting to use plsr which is part of the pls package in r. I amconducting analysis on datasets to identify which proteins/peptides are responsible for the variance between sample groups (Biomarker Spoting) in a multivariate fashion. I have a dataset in R called "FullDataListTrans". as you can see below the structure of the data is 40 different rows representing a sample and 94,272 columns each representing a p...

Hello, I have a data frame consisting of four columns and would like to sort based on the first column and then write the sorted data frame to a file. > df <- read.table("file.txt", sep="\t") where file.txt is simply a tab-delimited file containing 4 columns of data (first 2 numeric, second 2 character). I then do, > df_ordered <- df[order(df$V1), ] OR,

Hi there, I am a beginner. I would like to change the error bars in the bargraph.CI function from the default (se) to (sd). The help file says ci.fun= function(x) c(fun(x)-se(x), fun(x)+se(x)) Is there a simple way of telling the function what (x) precisely is - I already define in in the of the bargraph.CI function and assume that is should be able to use that information. cheers, Herwig --

...s some sample code of the idea I'm trying to accomplish: notes=c("Repressible alkaline phosphatase, a glycoprotein localized to the vacuole; regulated by levels of inorganic phosphate and by a system consisting of Pho4p, Pho9p, Pho80p, Pho81p and Pho85p; dephosphorylates phosphotyrosyl peptides") par(mar=c(10,3,10,3)) image(as.matrix(c(1,2,3,4,5))) mtext(strwrap(notes, width=60), line=5, side=3) ..as you can see, the long text plots over itself and doesn't wrap. Does anyone know how to include a paragraph in the margins? Thanks in advance! --Jake

Hi I am analysing a dataset of 40 samples each with 90,000 intensity measures for various peptides. I am trying to identify the Biomarkers (i.e. most significant peptides). I beleive that PLS with jack knifing, or alternativeley CMV(cross-model-validation) are multivariateThe 40 samples belong to four different groups. I have managed to conduct the plsr using the commands: BHPLS1 <- pl...

Hi, I can run the code some days ago . But cant run now.  Problem 1: Output is ok ensembl = useDataset("hsapiens_gene_ensembl",mart=ensembl) utr5 = getSequence(chromosome=3, start=185514033, end=185535839, type="entrezgene",seqType="5utr", mart=ensembl)  Output :                                                                                                5utr

...ns: Carbamidomethyl (C)\nVariable modifications: Oxidation (M)\nCleavage by Trypsin: cuts C-term side of KR unless next residue is P\nNumber of mass value! s searched: <B>6</B>\nNumber of mass values matched: <B>1</B>\! nSequenc e Coverage: <B>8%</B>\n\nMatched peptides shown in <B><FONT COLOR=#FF0000>Bold Red</FONT></B>\n\n <B>1</B> MVCDKCEKKL SKVIVPDKWK DGARNVTEGG GRKINENKLL SKKNRWSPYS <B>\n 51</B> TCTTKCMICK QQVHQDGKYC HTCAYSK<B><FONT COLOR=#FF0000>GVC AMCGK</FONT></B>QVLDT KMYKQSNV\...

Dear all, As you can see from the attachment I'm using R to automatically annotate peptide fragmentation mass spectra, which are represented by impulse plots. I'd like to poll you on approaches of how to deal as generally as possible with the two biggest annotation issues I run into: 1) very close annotated masses (impulses) with similar y-axis dimensions - resulting in overlapping labels

On 09/07/2018 3:24 PM, Witold E Wolski wrote: > Dear Yihui, > > Thank you for the valuable questions. > > sample_analysis is a "tibble" while > configuration is an "R6" class. > But I also have parametrized reports where I pass R reference classes > as arguments. > > This is the Rmd yaml params part corresponding to the error message. > >

Dear all, I want to compute the average of the three blocks for each x-variable which is equal slide in the code below. How can I do that ? block x1 x2 x3 x4 x5 1 23 22 23 24 23 1 21 25 26 21 39 1 23 24 22 23 23 2 20 21 23 24 28 2 32 23 34 24 26 2 19

I'm not sure if I should bother you team with this, apologies in case it's a bother. I'm trying gcc 6.2.1 (from devtoolset-6) with R, everything seems to work just fine, except for mzR. Here is failed build: g++ -m64 -shared -L/usr/lib64/R/lib -Wl,-z,relro -o mzR.so cramp.o ramp_base64.o ramp.o RcppRamp.o RcppRampModule.o rnetCDF.o RcppPwiz.o RcppPwizModule.o RcppIdent.o

Dear Duncan, Was close to giving up to use the parameterized rmarkown as vignettes. But your suggestions to use quote and eval, as well as to use the package parameter in data made it work, with all devtools::install,check,build and build_vignettes as well as with R CMD ... etc. But most importantly it also still works with: rmarkdown::render("vignettes/tr_srm_summary.Rmd",

Dear Colleague, Happy New Year! As we know, codon preference among different species could be dramatically different. To enhance the expression level of a foreign protein in a particular expression system (E.coli, Yeast, Insect, or Mammalian cell), it is very important to adjust the codon frequency of the foreign protein to match that of the host expression system. One classic example is GFP

http://www.softgoeshome.com/ Microsoft Windows XP Professional - 50 Adobe Photoshop 7.0 - 60 Microsoft Office XP Professional - 100 Microsoft Windows 2000 Professional - 50 Adobe PageMaker 7.0 - 60 Adobe Illustrator 10 - 80 Corel Draw Graphics Suite 11 - 120 Norton Antivirus 2004 Professional - 15 Borland Delphi 7 Professional - 70 Adobe Acrobat 6.0 Professional - 100 Adobe Acrobat 6.0