search for: uncur

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2011 Jun 07
1
Creating a file with reusable functions accessible throughout a computational biology cancer project
...that I can call these functions from within the sub-folders in each type of cancer. My confusion is that I'm not sure of the syntax to make this happen. For example: Within the "Prostate_Cancer" folder, I have the following folders: "curated" AND "src" AND "uncurated" Within "uncurated" I have a ton of files, one of which could be: PMID5377_fullpdata.csv within "src" I have my R scripts, the one corresponding to the above "uncurated" file would be: PMID5377_curation.R Here's the problem I'm trying to address: Ma...
2011 Jun 02
2
Matrix Question
...represent stage and "N's" represent degree of disease spreading. I want to create output that looks like this: *Sample_Output_File* T N 1 0 2 1 0 0 1 0 0 3 As it currently stands, my code is the following: rm(list=ls()) source("../../functions.R") uncurated <- read.csv("../uncurated/Sample_Input_File_full_pdata.csv",as.is =TRUE,row.names=1) ##initial creation of curated dataframe curated <- initialCuratedDF(rownames(uncurated),template.filename="Sample_Template_File.csv") ##-------------------- ##start the mappings ##--...
2011 Sep 16
3
Problematic If-Else statement
Hi guys, My code (next 2 lines below) isn't doing what I'm expecting it to: tmp <- ifelse(uncurated$days_to_tumor_recurrence=="null","norecurrence","recurrence") curated$recurrence_status <- tmp I want the column "recurrence_status" in my output file to have values "recurrence" (if the input value had a number in the days_to_tumor_recurren...
2012 Jul 24
9
Regular Expression
...2002 I want to make output like so: MONTH QUARTER YEAR 07 3 2012 07 3 2001 01 1 2002 I was having some trouble getting the regular expression to work. I think it should be something like the following: tmp <- uncurated$MONTH *tmp <- gsub("[^-\\d\\d]","",tmp,perl=TRUE)* *tmp[tmp=="-"] <- ""* *curated$MONTH <- tmp* * * tmp <- uncurated$QUARTER *tmp <- gsub("[^-\\d]","",tmp,perl=TRUE)* *tmp[tmp=="-"] <- ""* *curated...
2012 Feb 28
1
Error in read.table(file = file, header = header, sep = sep, quote = quote, : more columns than column names
...ings came up. I followed the leads and read the ?read.delim page; I tried changing header = TRUE, and row.names = TRUE-- but I've still been having trouble fixing it, so I would greatly appreciate any help you can provide. Here is my code: rm(list=ls()) source("../../functions.R") uncurated <- read.csv("../uncurated/GSE3141_full_pdata.csv", as.is =TRUE,row.names=1) celfile.dir <- "../../../DATA/GSE3141/RAW" ##initial creation of curated dataframe curated <- initialCuratedDF(rownames(uncurated), template.filename="template.csv") The error o...