search for: breast

Displaying 20 results from an estimated 154 matches for "breast".

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2010 May 06
5
Apologies : question on transforming a table
...forward 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 pheno 1 A Breast Cancer 2 A Appendicitis 3 A Microcephaly 4 B Polyps 5 B Autism 6 C Autism 7 D Breast Cancer 8 D Polyps 9 D Appendicitis 10 E Breast Cancer What I want is this : ID Breast Cancer Appendicitis Microcephaly Polyps Autism A 1 1 1 B 1 1 C 1 D...
2017 Jul 12
0
Extracting sentences with combinations of target words/terms from cancer patient text medical records
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 <- "([^.?!]*(?=[^.?!]*\\bbreast\\b)(?=[^.?!]*\\b(metastatic|stage IV)\\b)(?=[\\s.?!])[^.?!]*[.?!])" > regmatches(txt,...
2017 Jul 13
1
Extracting sentences with combinations of target words/terms from cancer patient text medical records
...es, how would you go about it? Thanks, Paul library(tidyverse) library(stringr) library(lubridate) sentence_match <- function(x){ sentence_extract <- str_extract_all(x, boundary("sentence"), simplify = TRUE) sentence_number <- intersect(str_which(sentence_extract, "breast"), str_which(sentence_extract, "metastatic|stage IV")) sentence_match <- str_c(sentence_number, ": ", sentence_extract[sentence_number], collapse = "") sentence_match } sampletxt <- structure( list( PTNO = c(1, 2, 2, 2), DATE = struct...
2010 Jun 18
2
help with reshape is needed again!
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 following format: patientID gene1 gene2 gene3 gene4............ -----...
2017 Jul 12
2
Extracting sentences with combinations of target words/terms from cancer patient text medical records
...gt; >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 time since I used R and I feel a bit rusty. I wrote a function called "sentence_match" that seemed to work well when applied to a single piece of text. You can see that by running the section tit...
2010 May 23
3
"order" issue
...25 CO:SW_620 -1.53265 -1.35446 Colon 63 RE:CAKI_1 -2.48443 0.43245 Renal 39 LE:RPMI_8226 -2.59561 -1.9448 Leukemia 26 LC:A549 -2.66221 0.71215 Lung 61 RE:A498 -2.89402 0.93287 Renal 9 BR:HS578T -2.94118 1.1217 Breast 34 LC:NCI_H522 -2.94381 0.3859 Lung 66 RE:TK_10 -2.95281 1.26245 Renal 52 OV:NCI_ADR_RES -3.04456 0.17046 Ovarian 57 OV:SK_OV_3 -3.04477 2.15405 Ovarian 53 OV:OVCAR_3 -3.0705 -0.31743 Ovarian 14 CNS:SF_295 -3.09348 -1.00095...
2017 Jul 11
2
Extracting sentences with combinations of target words/terms from cancer patient text medical records
...o 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 time since I used R and I feel a bit rusty. I wrote a function called "sentence_match" that seemed to work well when applied to a single piece of text. You can see that by running the section titled &...
2017 Jul 13
0
Extracting sentences with combinations of target words/terms from cancer patient text medical records
...es, how would you go about it? Thanks, Paul library(tidyverse) library(stringr) library(lubridate) sentence_match <- function(x){ sentence_extract <- str_extract_all(x, boundary("sentence"), simplify = TRUE) sentence_number <- intersect(str_which(sentence_extract, "breast"), str_which(sentence_extract, "metastatic|stage IV")) sentence_match <- str_c(sentence_number, ": ", sentence_extract[sentence_number], collapse = "") sentence_match } sampletxt <- structure( list( PTNO = c(1, 2, 2, 2), DATE = struct...
2010 Jan 29
1
help on drawing right colors within a grouped xyplot (Lattice)
...;-xyplot(EGFR~EPHA2,data=Dataset,groups=interaction(Sens,Tissue),cex=c(1,3),pch=19) > update(obj, par.settings = + custom.theme(symbol = brewer.pal(9, "Paired"), + fill = brewer.pal(9, "Paired"))) > Here are the data: Tissue Sens EGFR ITGB1 1 Breast 1 8.389 12.867 2 Breast 1 3.441 9.636 3 Breast 3 8.286 12.732 4 Breast 3 9.059 12.296 5 Breast 3 7.076 10.519 6 CNS 1 8.068 12.189 7 CNS 1 7.909 11.255 8 CNS 1 7.311 10.259 9 CNS 3 8.337 11.360 10 CNS 3 7.691 12.108 1...
2017 Jul 11
0
Extracting sentences with combinations of target words/terms from cancer patient text medical records
...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 time since I used R and I feel a bit rusty. I wrote a > function called "sentence_match" that seemed to work well when applied to a > single piece of text. You can see that by running...
2008 Feb 19
0
Van't Veer paper on breast cancer
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 difficulties in building the classifier and I was wondering if someone else has worked on it and could give me some he...
2004 Mar 31
1
LARGE BREASTS Handoff back to * from * via IAX?
How do I do this 1) ZAP-> * -> IAX(1) ------> IAX(2) -----> DG104S ------> Handset 2) No Answer on Handset 3) Back to IAX(1) 4) IAX(1) tries a cell phone 5) Still no Answer 6) Local * Voicemail. I have 1 working, and I had 4 working when there was only one box, i.e. when the handset did not answer the DG, asterisk went to the next step. Now that I have step 1 going to another
2010 Jun 17
2
help for reshape function
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 value gene1 ----------------------------- gene1 1 10 10 gene1 2 20 20 gene1 3 50...
2007 Jun 06
2
Multiple color schemes for barchart (lattice)
...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 0 100.00000 PAX8 Brain.N(3) FALSE 6 3 100.00000 ESR1 (ER) Breast.M(11) TRUE 7 0 100.00000 PAX8 Breast.M(11) TRUE 8 0 36.36364 ESR1 (ER) Cervix.M(11) TRUE 9 1 9.09091 ESR1 (ER) Cervix.M(11) TRUE 10 2 18.18182 ESR1 (ER) Cervix.M(11) TRUE 11 3 36.36364 ESR1 (ER) Cervix.M(11) TRUE palette <- palette(gray(seq(0, 1,len=4))) trellis...
2005 Jun 22
1
analyzing suvival data using splines (a.k.a., piecewise log-hazard-ratio models)
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 ratio (or rate of failure for a specific time) as a function of the continuous covariate, as we...
2002 Jul 29
1
density estimation on 2-D bounded domain
Dear R experts, density estimation on a 2 dimensional bounded domain --------------------------------------------------------------------- I am currently trying to estimate the probability density (PD) of cancers within the breast using the sm library with the routine sm.density Of course a practical PD must be limited by the curve of the breast outline. I don't have a clue after perusing R documentation. !! Is there a way to calculate with R statistics !! (with sm.density, or otherwise) !! such a density with an imp...
2004 Oct 06
4
R2.0.0 bug in function vcov in library survival (PR#7266)
...o cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for a HTML browser interface to help. Type 'q()' to quit R. [Previously saved workspace restored] > rm(list=ls()) > load("~/R/wlh0301/data/breast.RData") > library(survival) Loading required package: splines > u2<-coxph(Surv(time,event) ~ age + cbmi + smoker + drink , data=breast.1) > tmp <- vcov(u2) Error in vcov(u2) : no applicable method for "vcov" > > class(u2) [1] "coxph"
2003 Sep 25
1
Diamond graphs, again.
...re empty, but in this case the values in the cells basically _are_ counts, so we are _not_ left wondering how much data each cell is based on. I have not yet seen the article this was based on. c. Figure 7 has two graphs. On the left it's relative risk of breast cancer as the thing to be explained, with adult weight change (measured in kg; why not as a proportion of starting weight?) and hormone use (never, past, current) as the explanatory variables. On the right excess risk is to be explained, with the same explanatory var...
2017 Sep 20
3
Network meta-analysis help
Greetings. I hope my message finds you well. I know this question may be silly for some experts like you but it's a very important matter for me so, sorry for that. I was trying to make a network meta-analysis using R for the attached data set which shows the association between breast feeding and autism spectrum disorder (the event here is bad). I've searched a lot through the internet but no clear guidelines on how to do network meta-analysis and produce the related figures (Forest plot, Network plot, Heat map .... ect). I've installed "netmeta" pack success...
2012 Jan 03
0
Job opportunity in AMSTERDAM: ANALYSIS OF NGS CANCER DATA
...large panels of human tumors, on which we are currently performing kinase exon sequencing. More specifically, we are performing sequencing on 1) 400 samples from the NEO-ALTTO study to find alterations associated with resistance to HER2 targeted therapies; 2) at least 200 colorectal samples and 300 breast cancers (triple negatives and invasive lobular carcinomas) to detect alterations frequently occurring in these patient populations. A very strong feature of all these datasets is that matched controls are available to ensure high accuracy in variant calling. The goal is to detect genomic alteration...