similar to: how to extract the 1st field from a vector of strings

Through converting a miRNAs file from FASTA to character format I get a vector which looks like the following: > nml [1] "hsa-let-7a MIMAT0000062 Homo sapiens let-7a" [2] "hsa-let-7b MIMAT0000063 Homo sapiens let-7b" [3] "hsa-let-7c MIMAT0000064 Homo sapiens let-7c" [4] "hsa-let-7d MIMAT0000065 Homo sapiens

> chromosomes id refseq name length 1 0 NC_000001.9 Homo sapiens chromosome 1 247249719 2 1 NC_000002.10 Homo sapiens chromosome 2 242951149 3 2 NC_000003.10 Homo sapiens chromosome 3 199501827 4 3 NC_000004.10 Homo sapiens chromosome 4 191273063 5 4 NC_000005.8 Homo sapiens chromosome 5 180857866 6 5 NC_000006.10 Homo sapiens chromosome 6

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

Hi ALL, I have very simple question regarding pattern matching. Could anyone tell me how to I can use R to retrieve string pattern from text file. for example my file contain following information SpeciesCommon=(Human);SpeciesScientific=(Homo sapiens);ReactiveCentres=(N,C,C,C,+ H,O,C,C,C,C,O,H);BondInvolved=(C-H);EzCatDBID=(S00343);BondFormed=(O-H,O-H);Bond+

Hi R-users, I have a data frame like this: photographer category picture points Hannu kalat limamikko 1 Teemu kalat verkkovaja 3 Hate kalat munat puoliks padassa 6 Hannu kalat isokala 8 Teemu kasvit, sienet ja muut eliöt harppi 2 Hate kasvit, sienet ja muut eliöt pyynikki 2 Petteri kasvit, sienet ja muut eliöt harmaaleppä 5 Lauri kasvit, sienet ja muut eliöt lumipuu 9 Teemu linnut kainostelua 1

On 13 October 2015 at 16:41, Rafael Espíndola <llvm-dev at lists.llvm.org> wrote: >> - *Be welcoming.* We strive to be a community that welcomes and supports >> people of all backgrounds and identities. This includes, but is not limited >> to members of any race, ethnicity, culture, national origin, colour, >> immigration status, social and economic class, educational

Hi, Am am plotting aggregated frequency data (extracted from an RDBMS) relating to DNA sequence features for each of the human chromosomes as described in the table chromosomes below (the frequency data is in a table 'hits' that has a value (or not) for each of a set of bins across each chromosome). I would like to mark the extent of the chromosome (according to the length value in

Hi R-users, I have a dataset like this: kuvaaja kuva yhteispisteet Hannu isokala 8 Hannu kaapin alta löytynyt 2 Hannu kaapin alta löytynyt 2 8 Hannu limamikko 1 Hannu maukasta marmeladia 8 Hannu skrinnareita 4 Hate madekoukkujen suojelupyhimys 3 Hate matka aikaan joka ei enää palaa 3 Hate munat puoliks padassa 6 Hate pyynikki 2 Hate vailla armeerausta 2

Dear all, I have data.frame object in R. I want to export it in tab-delimited file with several lines of header initiated with comment sign (#). I do not know how to do that in R. Could you please give helps on this problem? Thanks in advance. Best, Jian-Feng, ################################################################## The lines I want to write in the header lines look like, with words

I deal with a huge amount of Biology data stored in different databases. The databases belongig to Bioconductor organization can be accessed through Bioconductor packages. Unluckily some useful data is stored in databases like, for instance, miRDB, miRecords, etc ... which offer just an interactive HTML interface. See for instance http://mirdb.org/cgi-bin/search.cgi,

Hi guys, one of the questions where you need a real human instead of a search engine, so it would be great if you could help. I have a matrix of z-scores which I would like to filter, sometimes columnwise, sometimes rowwise. Data looks like this: Allstar hsa.let.7a hsa.let.7a.1 hsa.let.7a.2 2 0.87 0.79 -0.57 1.07 3 0.67 -1.14 -0.78 -0.95 4

Hello list. I have a vector of values: eg > head(diff_mirs_list) [1] "hsa-miR-26b" "hsa-miR-26b" "hsa-miR-23a" "hsa-miR-27b" "hsa-miR-29a" [6] "hsa-miR-29b" and I would like to conditionally replace each value in this vector with a number defined in a dataframe: > fc ???????????? Probe ave.fc 1?????? hsa-let-7a?? 1.28 2?????

I have the following list of strings: name <- c("hsa-miR-555p","hsa-miR-519b-3p","hsa-let-7a") What I want to do is for each of the above strings replace the text after second delimiter with "zzz". Yielding: hsa-miR-zzz hsa-miR-zzz hsa-let-zzz What's the way to do it? [[alternative HTML version deleted]]

Hi, I have two questions want to ask. 1. If I have a matrix like this, and I want to figure out the rows whose value in the 3rd column are less than 0.05. How can I do it with R. hsa-let-7a--MBTD1 0.528239197 2.41E-05 hsa-let-7a--APOBEC1 0.507869409 5.51E-05 hsa-let-7a--PAPOLA 0.470451884 0.000221774 hsa-let-7a--NF2 0.469280186 0.000231065 hsa-let-7a--SLC17A5

Hi, When I look at the summary of an rpart object run on my data, I get 7 nodes but when I plot the rpart object, I get only 3 nodes. Should the number of nodes not match in the results of the 2 functions (summary and plot) or it is not always the same? Look forward to your reply, Carol -------------------------------------------- ?summary(rpart.res) Call: rpart(formula = mydata$class ~ ., data

Hi, There is a question that I am confused. I have a set of data like this: hsa-miR-205--GATA3 0.797882767 1.08E-13 hsa-miR-205--ITGB4 0.750217593 1.85E-11 hsa-miR-187--PGF 0.797604155 3.24E-11 hsa-miR-205--SERPINB5 0.744124886 3.28E-11 hsa-miR-205--PBX1 0.734487224 7.89E-11 hsa-miR-205--MCC 0.72499934 1.80E-10 hsa-miR-205--WNT5B 0.717705259 3.33E-10 hsa-miR-200c--PKN2 0.721746815

Hello everyone, Im working with graphNEL object and want to extract all the nodes which have adjacent nodes with at least 20 nodes in between them. acc(graph, graphnodes) obviously provides a list for the accessable nodes of every node from a node and a number of the edges between them. Like this: $`hsa:8379` hsa:100131844 hsa:10393 hsa:246184 hsa:29882 hsa:29945 1

*I have the following function:* /plot_mi_time = function(mdata, miname) { mdata2 = mdata[row.names(hakat) == miname, ] print(mdata2) xcoords <- c(1,1,2,2,3,3,4,4,5,5,6,6) plot(c(xcoords), mdata2, xaxt="n", ylab="Expression", xlab="Time(h)", , main=miname) axis(1, at=xcoords,

Hi all, I have samba server 2.2.8a to act as a PDC on a mixed WinXP/Win2k/WinNT network. I joined all my workstations to the domain with no problem... And users can login into the domain and access their folders/printers, BUT!!! Every now and then they cannot log in getting error message that domain controller cannot be found.... I'm trying to track the problem down :-) When I went thru

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 ?