search for: protein

...of the R object I want to create, and the type of functions I am using to do it. I hope that one of you will be able to point me towards a better and quicker way of doing the parsing! Here is the (simplified) structure of the relevant nodes of the xml file: <model> (many many nodes) <protein> (a couple of proteins per model node) <peptide> (1 per protein node) <domain> (1 or more per peptide node) <aa> (0 or more per domain node) </aa> </domain> </peptide> </protein> </model> Here is the basic str...

Dear R-developers, I came to a somewhat unexpected behaviour of read.csv() which is trivial but worthwhile to note -- my data involves a protein named "1433E" but to save space I drop the quote so it becomes, Gene,SNP,prot,log10p YWHAE,13:62129097_C_T,1433E,7.35 YWHAE,4:72617557_T_TA,1433E,7.73 Both read.cv() and readr::read_csv() consider prot(ein) name as (possibly confused by scientific notation) numeric 1433 which only alert...

What I am trying to do is use GUI function, traitr, and to call for a pdb file and save it and then display it. I want to call for it by taking it from the user and then displaying it on the screen. I am having problems with that. The line pdb <- read.pdb(""ProteinCode) where proteincode should be the name of the protein, for example 1ly2, but it always ends up being protein. My question is how to you make the input for read.pdb actually be the input by the user and not protein code. I want to be able to type 1ly2, and for the program to actually display the...

Hi, I have the following data file to be parsed and captured as a data frame: __DATA__ #GDS_ID GENE_NAME GENE_DESCRIPTION GENE_FUNCTION 1007_s_at | DDR1 | discoidin domain receptor tyrosine kinase 1 | protein-coding 1053_at | RFC2 | replication factor C (activator 1) 2, 40kDa | protein-coding 117_at | HSPA6 | heat shock 70kDa protein 6 (HSP70B') | protein-coding __END__ In particular it is separated by " | " , namely - space, bar, space. However I tried this without avail: geneinfo <...

Dear all, Here is my code which am using to combine 5th column from different data sets. Here is the function to do my job genesymbol.append.file <-NULL gene.column <- NULL readGeneSymbol <- function(files,genesymbol.column=5){ for(i in fnames){ temp <- read.table(fnames,header=T,sep="\t",stringsAsFactors=F,quote="\"")

.../www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=full_report&list_uids=18111" #obtain the exprs matrix for cluster analysis #ask questions DEG_files <- grep("bak", dir());#pay attention to the filenames exprs_files <- grep("copy", dir()); protein <- c(); assign_exprs <- function(files, protein) { #use to find the DEGs or exprs for cmeans clustering for(i in 1:length(files)) { microarray_data <- read.csv(file = files[i], header = T, sep = "\t"); microarray_data[, 7] <- gsub("([\\s\\S]+gene_n...

My laboratory is measuring the abundance of various proteins in the blood from either healthy individuals or from individuals with various diseases. I would like to determine which proteins, if any, have significantly different abundances between the healthy and diseased individuals. Currently, one of my colleagues is performing an ANOVA on each protein w...

Dear R-helpers: thank your for your attention. i am a newer to R and i am doing some protein category classification based on the amino acid sequence.while i have some questions urgently. 1. any packages for analysis amino acid sequence 2. given two sequences "AAA" and "BBB",how can i combine them into "AAABBB" 3. based on "AAABBB",how can i get s...

?s 11:46 de 16/04/2024, jing hua zhao escreveu: > Dear R-developers, > > I came to a somewhat unexpected behaviour of read.csv() which is trivial but worthwhile to note -- my data involves a protein named "1433E" but to save space I drop the quote so it becomes, > > Gene,SNP,prot,log10p > YWHAE,13:62129097_C_T,1433E,7.35 > YWHAE,4:72617557_T_TA,1433E,7.73 > > Both read.cv() and readr::read_csv() consider prot(ein) name as (possibly confused by scientific notation)...

.../human-genes-rename-microsoft-excel-misreading-dates On Tue, Apr 16, 2024 at 3:46?AM jing hua zhao <jinghuazhao at hotmail.com> wrote: > > Dear R-developers, > > I came to a somewhat unexpected behaviour of read.csv() which is trivial but worthwhile to note -- my data involves a protein named "1433E" but to save space I drop the quote so it becomes, > > Gene,SNP,prot,log10p > YWHAE,13:62129097_C_T,1433E,7.35 > YWHAE,4:72617557_T_TA,1433E,7.73 > > Both read.cv() and readr::read_csv() consider prot(ein) name as (possibly confused by scientific notation) n...

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 (green fluorescent protein) which was optimized to achieve high-level of e...

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 (green fluorescent protein) which was optimized to achieve high-level of e...

Hi, I have the following data frame: > print(mydatframe) __DATAFRAME__ V1 V2 V3 1 1007_s_at DDR1 discoidin domain receptor tyrosine kinase 1 2 1053_at RFC2 replication factor C (activator 1) 2, 40kDa 3 117_at HSPA6 heat shock 70kDa protein 6 (HSP70B') __END__ Is there a way to create a hash with V2 as Key and V3 as its value? - Gundala Viswanath Jakarta - Indonesia

Dear R users, I would like to align two protein sequences using BLAST (bl2seq). The question is whether this programm have been implemented in R. Thank you for your help, Alla.

...777 12.8720763 13.10863036 12.97146724 13.15723934 -------------- next part -------------- Probe ID Transcript ID InterPro Domains Panther Families Panther Biological Process Level 1 Panther Biological Process Level 2 A_51_P100034 NM_027162.3 MIF4G-likes type 3,MIF4-likes type 1/2/3 EIF4G DOMAIN PROTEIN,AD023 PROTEIN Protein metabolism and modification Protein biosynthesis A_51_P100052 NM_198863.1 Leucine-rich repeats typical subtype,Leucine-rich repeat,Leucine-rich repeats cysteine-rich flanking regions N-terminal,Cysteine-rich flanking regions C-terminal LEUCINE-RICH TRANSMEMBRANE PROTEINS...

Hi dear R community, I have up to 12 measures of a protein for each of 6 patients, taken every two or three days. The pattern of the protein looks periodic, but the height of the peaks is highly variable. It's something like this: patient <- data.frame( day = c(1, 3, 5, 8, 10, 12, 15, 17, 19, 22, 24, 26), protein = c(5, 3, 10, 7, 2, 8, 25, 12,...

Hi all, I have thousands of strings like these ones: "1159_1; YP_177963; PPE FAMILY PROTEIN" "1100_13; SECRETED L-ALANINE DEHYDROGENASE ALD CAA15575" "1141_24; gi;2894249;emb;CAA17111.1; PROBABLE ISOCITRATE DEHYDROGENASE" and various others.. I'm interested to extract the code for the protein (in this example: YP_177963, CAA15575, CAA17111). I found...

Hi, Suppose I have the following tabular data: 1729_at | TRADD | TNFRSF1A-associated via death domain | protein-coding 1773_at | FNTB | farnesyltransferase, CAAX box, beta | protein-coding 177_at | PLD1 | phospholipase D1, phosphatidylcholine-specific | protein-coding What is the right separator used for read.table function? I tried this: dat <- read.table("geo2geneinfo_bymodel.txt", sep = &...

Dear All, I need to fetch GO ontologies for Homo sapiens with their mappings to corresponding Uniprot identifiers. I would be using this information to compare result from a clustering algorithm with existing protein complexes. This would be a test to check how the clustering algorithm accurately captures GO terms with respect to the known protein complexes. Can anyone suggest a simple workflow with the requisite packages? I am trying to find out to fetch GO ontologies for homo sapiens with bioconductor but mos...

Dear all, I try to use read.table to get the data from a tab delimited file, and some of the data is shown below: 3185 heterogeneous nuclear ribonucleoprotein F 3187 heterogeneous nuclear ribonucleoprotein H1 (H) 3188 heterogeneous nuclear ribonucleoprotein H2 (H') 3189 heterogeneous nuclear ribonucleoprotein H3 (2H9) 3190 heterogeneous nuclear ribonucleoprotein K /// heterogeneous nuclear ribonucleoprotein K 3190 heterogeneous nuclear...