similar to: density estimation on 2-D bounded domain

COMPUTATIONAL ANALYSIS OF NEXT GENERATION SEQUENCE DATA (http://bioinformatics.nki.nl/vacancies.php) THREE BIOINFORMATICS POSITIONS PROJECT OUTLINE Genomic alterations are major determinant of responses to (targeted) therapies in cancer. In fact, the best positive and negative predictors of responses to targeted therapies are alterations in kinases or their direct downstream effectors. To

Hi Paul, No need to collapse the information into a single text string, gregexpr() can take a vector of strings (sentences in your case). You can split your sentences up, number them how you want, then search for your pattern either via regex or via these extra packages you use which probably use the PCRE regex library anyway. However, as this is basically what you did, I'm not sure why

Hi Robert, Thank you for your reply. An attempt to solve this via a regular expression query is particularly helpful. Unfortunately, I don't have much time to play around with this just now. Ultimately though, I think I would like to implement a solution something along the lines of what you have done. I have a book on regular expressions that I am now starting to read. In the meantime, the

Hi everyone, I connected a data in FileMaker server with odbcConnect. When I call the data "CANCERS" using sqlFetch, it looks okay. However, the number of obs was different with the actual number. If I read the same data from Microsoft Access, there are 656 obs. in it but srt() shows me 600 obs. Does anyone know why this happened and how to read all obs. from R? Thank you in advance.

Dear R-help list, Apologies. I am trying to convert one table to another. It feels that it should be a very straightforward answer with a single (or two) commands with the right extensions, but I really can't figure this out right now. I have several hundred pheno factors actually, so manually doing this line by line is not an option. My original table is approximately like this : ID

hi, folks: i need to transpose the following data: gene tissue patient1 patient2 patient3..... --------------------------------------------- gene1 breast 10 100 1 gene2 breast 20 200 4 gene3 breast 30 50 5 gene4 breast 40 400 9 ................................ to the

Hi, I've lost my mind on it... I have to scatterplot two vectors, grouped by a third variable, with two different dimensions according to whether each cell line in the plot is sensitive or resistant to a given drug, and with a different color for each of 9 tissues of origin. Here's what I've done:

Have you looked at the CRAN Natural Language Processing Task View? If not, why not? If so, why were the resources described there inadequate? Bert On Jul 11, 2017 10:49 AM, "Paul Miller via R-help" <r-help at r-project.org> wrote: > Hello All, > > I need some help figuring out how to extract combinations of target > words/terms from cancer patient text medical

Hi Paul, Sounds like you have your answer, but for fun I thought I'd try solving your problem using only a regular expression query and base R. I believe this works: > txt <- "Patient had stage IV breast cancer. Nothing matches this sentence. Metastatic and breast match this sentence. French bike champion takes stage IV victory in Tour de France." > pattern <-

Hello All, I need some help figuring out how to extract combinations of target words/terms from cancer patient text medical records. I've provided some sample data and code below to illustrate what I'm trying to do. At the moment, I'm trying to extract sentences that contain the word "breast" plus either "metastatic" or "stage IV". It's been some

Hi Bert, Thanks for your reply. It appears that I didn't replace the variable name "sampletxt" with the argument "x" in my function. I've corrected that and now my code seems to be working fine. Paul ________________________________ From: Bert Gunter <bgunter.4567 at gmail.com> Cc: R-help <r-help at r-project.org> Sent: Tuesday, July 11, 2017 2:00 PM

hi, everyone: i have a question on the reshape function. i have the following dataset : gene tissue patient1 patient2 patient3............. _________________________________________________ gene1 breast 10 20 50 gene2 breast 20 40 60 gene3 breast 100 200 300 which i hope to convert to the following format: gene patientID

Hi everybody, this is a real dummy thing. I sorted a matrix based on a given column, and what I get is right, until it comes to columns of negative and positive values; than, "order" orders everything from max to min in the negative values, and then AGAIN from max to min in the positive values!!! Why isn't everything order from max to min, and that's it? Thank you!!! Attached

I'm looking for software that makes plots such as fig 4 (a)-(e), fig 5 anf fig 7 of Gray, Robert, "Flexible Methods for Analyzing Survival Data Using Splines, with Applications to Breast Cancer Prognosis," 1992, J Am Stat Assoc, pp 942-51. In other words, I'm looking for software that takes survival data and a continuous covariate as input and computes a curve giving log hazard

Hi, Is there a function in R that I can use to fit the data with skew t distribution? Speaking in detail, I first used the kernel density estimation to fit my data, then I drew the skew t using my specified location, scale, shape, and df to make it close to the kernel density. Now I want to get the parameter estimations of the skew t which give me the closet density to the kernel density.

Hello R-help. I am trying to make a stacked barplot where the color of the sections of each bar depend on another variable. > myData[1:11,] score percent marker cellType Malignant 1 0 100.00000 ESR1 (ER) Bladder.M(5) TRUE 2 0 80.00000 PAX8 Bladder.M(5) TRUE 3 1 20.00000 PAX8 Bladder.M(5) TRUE 4 0 100.00000 ESR1 (ER) Brain.N(3) FALSE 5 0

Full_Name: Sven Sandin Version: 2.0.0 OS: SuSE Linux 9.0 Submission from: (NULL) (81.227.17.135) Have just compiled and installed R-2.0.0.tar.gz running SuSE9.0. The function vcov do not accept "coxph" object as input any longer. The same R-program running R1.9.1 do work. R-program attached below. Exporting the coxph object from R2.0.0 to R1.9.1 I get vcov ouput in R1.9.1. Exporting

Hello all, I am working at the FORTH institute in Crete and it's been a long now that I am trying to reproduce the results of the paper : "Gene expression profiling predits clinical outcome of breast cancer", by Van't Veer et al. It has been published in NATURE, vol 415, 31 January 2002. http://www.nature.com/nature/journal/v415/n6871/full/415530a.html I am facing some

Research Assistant/Staff Scientist: Technology in Environmental Health (Silent Spring Institute; Boston, MA) Silent Spring Institute is a non-profit scientific research group studying the environment and health. We are a multi-disciplinary team and international leader in research on everyday exposures to hormone disruptors, tests for breast carcinogens, and environmental links to breast cancer.

On 08/27/15 12:12, Alice Wonder wrote: > On 08/27/2015 08:58 AM, g wrote: >> On 08/27/15 09:31, m.roth at 5-cent.us wrote: >> <> >> >>> *sigh* >>> And they're probably sent by a script running on the PC of a fat, >>> 47 yr old guy living in a basement and making money this way.... >>> >> . >> i seriously doubt it.