Displaying 5 results from an estimated 5 matches for "uncurated".
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curated
Creating a file with reusable functions accessible throughout a computational biology cancer project
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:
Many o...
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_recurrence c...
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$QUARTER
*tmp <- gsub("[^-\\d]","",tmp,perl=TRUE)*
*tmp[tmp=="-"] <- ""*
*curated$QUA...
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 occur...