similar to: writing to a file

Dear all, I am a R beginner, and I am looking for a way to do the same thing for all levels of a column in a table. Basically, I have a bunch of protein sequences composed of different amino acid residues, and each residue is represented by an uppercase letter. I want to calculate the ratio of different amino acid residues at each position of the proteins. Here is an example table: Proteins

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

Hello everyone, I would like to parse very large xml files from MS/MS experiments and create R objects from their content. (By very large, I mean going up to 5-10Gb, although I am using a 'small' 40M file to test my code.) My first attempt at parsing the 40M file, using the XML package, took more than 2200 seconds and left me quite disappointed. I managed to cut that down to around 40

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 with MS Excel. I would like to analyze

?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 >

Gene names being misinterpreted by spreadsheet software (read.csv is no different) is a classic issue in bioinformatics. It seems like every practitioner ends up encountering this issue in due time. E.g. https://pubmed.ncbi.nlm.nih.gov/15214961/ https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1044-7 https://www.nature.com/articles/d41586-021-02211-4

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 some

Hello group, I am learning R and I am new to many concepts.I face the following errors when I am trying to execute the following. I have 4 text files with protein accession numbers. I wanted to represent them in a venn diagram and for that I using intersect and setdiff functions. My data looks like this: file1.txt (c): NP_000005 NP_000020 NP_000030 NP_000053 file2.txt(e): NP_000005 NP_000020

The build system rolled up R-4.3.3.tar.gz and .xz (codename "Angel Food Cake") this morning. This is a minor update, intended as the wrap-up release for the 4.3.x series. This also marks the 6th anniversary of R-1.0.0. (2000-02-29) The list below details the changes in this release. You can get the source code from https://cran.r-project.org/src/base/R-4/R-4.3.3.tar.gz

The build system rolled up R-4.3.3.tar.gz and .xz (codename "Angel Food Cake") this morning. This is a minor update, intended as the wrap-up release for the 4.3.x series. This also marks the 6th anniversary of R-1.0.0. (2000-02-29) The list below details the changes in this release. You can get the source code from https://cran.r-project.org/src/base/R-4/R-4.3.3.tar.gz

The build system rolled up R-4.3.3.tar.gz and .xz (codename "Angel Food Cake") this morning. This is a minor update, intended as the wrap-up release for the 4.3.x series. This also marks the 6th anniversary of R-1.0.0. (2000-02-29) The list below details the changes in this release. You can get the source code from https://cran.r-project.org/src/base/R-4/R-4.3.3.tar.gz

Hi everybody, I am having a problem building a ROC curve with my data using the ROCR package. I have 10 lists of proteins such as attached (proteinlist.xls). each of the lists was calculated with a different p-value. The goal is to find the optimal p-value for the highest number of true positives as well as lowaest number of false positives. As far as I understood the explanations from the

Hi, I have a question about logistic regression in R. Suppose I have a small list of proteins P1, P2, P3 that predict a two-class target T, say cancer/noncancer. Lets further say I know that I can build a simple logistic regression model in R model <- glm(T ~ ., data=d.f(Y), family=binomial) (Y is the dataset of the Proteins). This works fine. T is a factored vector with levels cancer,

Hi, I'm wondering if anybody could possibly help me? I have a table with 5 tab-delimited columns. Each column has 'e-value' scores for 5 different proteins. I'd like to plot a distribution curve using hist() for the 5 different proteins and show the 5 distribution curves on the same graph in different colours. In the case, E-values will be the X-axis and frequency will be the

Dear R wizards, I am seeking advice on graphics in R. Specifically, how to manipulate the size and save a plot I have produced using the LDheatmap library. I confess I am relatively new to graphics in R, but I would greatly appreciate any suggestions you may have. LDheatmap produces a coloured triangular matrix of pairwise associations between 600 genetic markers in my dataset.

/Dear all,/// /I am very thankful, if you could tell what is the right way to write: mtext(paste(expression("R"^2),round(marco2[1,i],digits=3)," N? of proteins:",marco3[i]),side=4,cex=.6) in this case the output is: "R"^2 I tried also in this way: mtext(paste(expression(paste("R"^2)),round(marco2[1,i],digits=3)," N? of

Hi, perhaps you can help me to find out, how to find the best Lambda in a LASSO-model. I have a feature selection problem with 150 proteins potentially predicting Cancer or Noncancer. With a lasso model fit.glm <- glmpath(x=as.matrix(X), y=target, family="binomial") (target is 0, 1 <- Cancer non cancer, X the proteins, numerical in expression), I get following path (PICTURE

Dear All, I have two matrices A (40 x 732) and B (40 x 1230) and would like to calculate correlation between them.  I can use: cor(A,B, method="pearson") to calculate correlation between all possible pairs. But the issue is that there is one-many specific mappings between A and B and I just need to calculate correlations for those pairs (not all). Some variables in A (proteins, say p1)

Oct 21 10:04:05 alchemy dovecot: imap-login: Login: user=<paulproteus>, method=PLAIN, rip=127.0.0.1, lip=127.0.0.1, TLS Oct 21 10:05:44 alchemy dovecot: IMAP(paulproteus): file message-decoder.c: line 289 (message_decode_body): assertion failed: (pos < input->size) Oct 21 10:05:44 alchemy dovecot: IMAP(paulproteus): Raw backtrace: imap [0x80c8e10] -> imap [0x80c8d1c] ->

All Is there a package or library that will, given a nucleotide sequence 1. calculate the extinction coefficient at 260 nm for (Beer-Lambert's law) 2. calculate molecular weight 3. return it's complementary sequence I was able to find several packages that can do similar calculations for an amino acid sequence for proteins but none for nucleic acids. Any pointers, etc. would be