similar to: R 4.3.3 is released

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

?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

Hum... This boils down to > as.numeric("1.23e") [1] 1.23 > as.numeric("1.23e-") [1] 1.23 > as.numeric("1.23e+") [1] 1.23 which in turn comes from this code in src/main/util.c (function R_strtod) if (*p == 'e' || *p == 'E') { int expsign = 1; switch(*++p) { case '-': expsign = -1; case

Hello, Is there a faster way to do this? Basically, I'd like to NA all values in all_data if there are no 1's in the same column of the other matrix, iu. Put another way, I want to replace values in the all_data columns if values in the same column in iu are all 0. This is pretty slow for me, but works: all_data = matrix(c(1:9),3,3) colnames(all_data) =

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

I all, is there a way with R to perform an exact permutation test to replace the wilcoxon test to compare paired series and/or to perform pairwise multiple comparisons for related series after a Friedman test ? Thanks Gilles

I have been trying to use R to gather some information from parsed log files (as part of examining some performance issues). I parsed the log files and put the data into an SQLite database, and then used RSQLite to load the data into R. The fields of interest are controller, action and total_time: controller and action have string values; total_time has a decimal value. I first did the

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

Hi, I am pretty new to R and I would apreciatte very much your help to solve my problem. I have 40 csv files that have the same structure, and I want to merge them into a single data frame. I already have load and combined all the cvs files into a large list, and I created two filenames <- list.files('data',full.names=TRUE) All_data <- lapply(filenames,function(i){ ###read cvs

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

> On Aug 22, 2017, at 11:31 PM, jagan krishnan via R-help <r-help at r-project.org> wrote: > > Hi all, > This is Jagan.i have been provided a task of analyzing sales data of a company in R programming...Just wanted to know,how can I pull Tally 9.1 software data into R programming dataframe. > Waiting eagerly for your inputs. > With Regards,Jagannathan Krishnan > Sent

Hi, I have a fairly complex object that I have written a print function for. Thus when I do print(results), the R console shows me a whole bunch of stuff already formatted. What I want to do is to take whatever print(results) shows to console and then put that in a file. I am doing this using the sink command. However, I am unsure as to how to "unsink". Eg, how do I restore output to

Hi all, This is Jagan.i have been provided a task of analyzing sales data of a company in R programming...Just wanted to know,how can I pull Tally 9.1 software data into R programming dataframe. Waiting eagerly for your inputs. With Regards,Jagannathan Krishnan Sent from Yahoo Mail on Android On Tue, Aug 22, 2017 at 10:47 AM, jagan krishnan<jagan.krishnan at yahoo.co.in> wrote: Hi

Hi, Inline below. > On Aug 24, 2017, at 5:22 AM, John Kane via R-help <r-help at r-project.org> wrote: > > > IIt might help to read the material at one or both of these links http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example > <snip> In this case, had Jagan spent about 30 seconds Googling for the application developer's

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

Your message seems unclear, and as evidence the respondents are giving various answers. You should provide a small sample of input and output data as it would look in R to avoid this kind of thrashing about. See [1][2][3] for guidance. Note that you also really need to figure out how to make sure your email program sends plain text, because HTML formatting WILL be stripped by the mailing list

Hello All, I have a data frame consisting of 4 columns (id1, id2, y, pred) where pred is the predicted value based on the glm function and my data frame is called "all". "data" is another data frame that has all data but I want to put together some important columns from my original data frame (data) into another data frame (all) as follows and I would like them to be sorted

IIt might help to read the material at one or both of these links http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example Reproducibility ? Advanced R. | | | | Reproducibility ? Advanced R. | | | On Thursday, August 24, 2017, 6:19:25 AM EDT, John Kane <jrkrideau at yahoo.ca> wrote: On Thursday, August 24, 2017, 1:50:13 AM EDT, David