similar to: How to prpare the input data to writeFASTA ? Examples of CharacterToFASTArecords ...

It looks like Biostrings function "writeFASTA" overwrites the output file at each run. It seems it does not support the "append" parameter. I have to generate one big file gathering a miRNA identifier and relative sequence followd by a variable number of dara records pertaining such a miRNA target genes transcription. Each record is made up of a 3'utr identifier

Sometimes the following function call causes a database exception: > gene.seq <- getSequence (id=gene.map[,"ensembl_transcript_id"], type="ensembl_transcript_id", + seqType="3utr", mart=hmart) I understand the above function must be called by try to capture the eventual error. WHat is not clear to me is how to realize that an

I executed the following lines several times from a script as well as pasting them in an R shell. Systematically biomaRt is failing. The problem is to extract the 3UTR sequences corresponding to a vector containing 1941 Ensembl Transcript numbers (some are duplicated ... is this s problem ?) Please, find the failing instructions in the following including the ENST vector Any suggestion is

Hi all, I'm having some trouble in understanding how to ste the Error() term in the aov() function when fitting a hierarchical ANOVA. I have data concerning the expression of 2 miRNAs in 3 different cell lines, with 2 different extraction methods. The data is organized as follows : Line Extraction Target Expression 1 BC54 miRNA RNU48 22.48 2 BC54 miRNA

Dear R-users, I'm using lattice package and function xyplot for the first time so you will excuse me for my inexperience. I'm facing quite a simple problem but I'm having troubles on how to solve it, I've read tons of old mails in the archives and looked at some slides from?Deepayan Sarkar but still can not get the point. This is the context. I've got data on 9 microRNAs, each

Hi everyone, I am trying to find a way to filter a table; If I am given for example the following table: > head(intra) chr miRNA start end strand ACC hsa_ID region region_start region_end gene_id transcrip_id 1 chr1 miRNA 1102484 1102578 + ACC="MI0000342"; ID="hsa-mir-200b"; exon 1102484 1102578 NR_029639 NR_029639 2 chr1

Hi all, I already posted this to seqinr-forum@lists.r-forge.r-project.org but since (so far) no reply was given, I decided to try my luck in this list too. Dear list. I wish (for my thesis work), to import tRNA data into R and have it aligned. My questions are: 1) What resources can I use for the data. 2) What commands might help me with the import/alignment. So far, I found two nice

Dear useRs, the seqinR package contains utilities to import and analyze biological sequence data. For a general introduction see this document: http://pbil.univ-lyon1.fr/software/SeqinR//vignette.pdf Please do not use r-help for questions about seqinR or r-bugs for bug report about seqinR. Use instead the seqinR diffusion list: http://pbil.univ-lyon1.fr/software/SeqinR//mailing.php?lang=eng A

Dear useRs, the seqinR package contains utilities to import and analyze biological sequence data. For a general introduction see this document: http://pbil.univ-lyon1.fr/software/SeqinR//vignette.pdf Please do not use r-help for questions about seqinR or r-bugs for bug report about seqinR. Use instead the seqinR diffusion list: http://pbil.univ-lyon1.fr/software/SeqinR//mailing.php?lang=eng A

Hi there, I wonder if there is a way of efficiently generating a correlation matrix of two expression matrices. I want to correlate miRNA and mRNA expression and used the following code: ##dat.mi miRNA expression matrix, dat.m mRNA expression matrix nc <- nrow(dat.mi) cor.mat <- data.frame(rep(NA,nrow(dat.m))) pval.mat <- data.frame(rep(NA,nrow(dat.m))) for(i in 1:nc) { cr <- vector()

Hi all! While I am trying to read .cel files with oligo package: afbatch=read.celfiles(list.celfiles()) I get an error: Package 'pd.mirna.1.0.2xgain' was not found in the BioConductor repository How can I overcome this? Thank you in advance

I wonder whether R provides an interface to access miRecords data. Particularly, I am looking for extracting humans miRNA and target genes sequences. All such information is stored in there in a set of structured web site pages (http://mirecords.umn.edu/miRecords) I would greatly appreciate any suggestion even about other data bases from where it is possible to get the same sort of data. I had a

Unluckily I dela with miRNA files whose name may contain the character "*". Because of the special meaning of "*" I have to remove it. I found out how to make list.files() extract only those file names which contain a "*" Namely: # list.files(pattern="\\*") Now I have to process all files whose name does NOT contain the character "*". I cannot

Dear Sir: > I am a chinese researcher who interested in miRNA, and I want to use R to analysis my data.I have download R-2.4.0-win32.exe and install it smoothly on my > computer,but when I want to use this software, error occurs,it shows" R for > > windows GUI front-end meet some problems" and the interface closese > automatically, I don't know what happen.

Dear All, I am analyzing the miRNA data set in which I have 817 unique probes for each they have 20 features each . I have to group the similar features and take the median across them so that I have a data with no repeats to perform invariant analysis . My data looks something similar format probename sample1 sample2 sample3 A 2.3 2.4 2.5 A

Hi, I have a question about heatmap. I have a data with row as microRNA and two columns are two cell expression values for these microRNA. So, like: cell1 cell2 miRNA1 1.5 3.4 miRNA2 1.3 2.4 ................... miRNA50 5 2.1 miRNA51 7.3 0.5 I want to see some miRNA are high in cell1 and low in cell2 but others are low in cell1 and high in cell2. I

Bioinformatics Scientist position in Maryland Description Title: Bioinformatics Scientist I/II - Translational Science Location - Gaithersburg, MD Contact: higgsb at medimmune.com ** Please do not send a CV if you do not have most of the qualifications listed below ** Local candidates preferred Major Duties and Responsibilities: We have an opening in the pharmacogenomics group within the

Hello dear R help group, I would like to download the tRNA data on: http://gtrnadb.ucsc.edu/download.html And then import it into R. Can anyone direct me as to how to do so? Thanks, Tal ---------------------------------------------- My contact information: Tal Galili E-mail: Tal.Galili@gmail.com Phone number: 972-52-7275845 FaceBook: Tal Galili My Blogs: http://www.talgalili.com (Web and

* Published in IEEE Xplore * Google Scholar H5-Index = 22 ------------------------------ ---- Doctoral Symposium of CISTI'2023 ------------------------------ ------------ CISTI'2023 - 18th Iberian Conference on Information Systems and Technologies 20 - 23 of June 2023, University of Aveiro, Aveiro, Portugal http://cisti.eu/

Hello List I'm moving this over from the bioC list as, although the problem I'm working on is biological, the current bottle neck is my poor understanding of R. I wonder if someone would help me with the following function. cumulMetric <- function(deMirPresGenes, deMirs){ ??? #need to match position of each miR in deMirPresGenes with its FC to form a vector of FC in correct order ?