Displaying 20 results from an estimated 1000 matches similar to: "How to import the large data into R"
2006 Apr 06
4
Reshaping genetic data from long to wide
Bottom Line Up Front: How does one reshape genetic data from long to wide?
I currently have a lot of data. About 180 individuals (some
probands/patients, some parents, rare siblings) and SNP data from 6000 loci
on each. The standard formats seem to be something along the lines of Famid,
pid, fatid, motid, affected, sex, locus1Allele1, locus1Allele2,
locus2Allele1, locus2Allele2, etc
In other
2011 Feb 03
1
bug in codetools/R CMD check?
Hi Mr Tierney,
I have noticed an error message from R 1.12.x's CMD check for a while (apparently prof Ripley completely rewrote CMD check in R 1.12+)
e.g.:
http://bioconductor.org/checkResults/2.7/bioc-LATEST/snpMatrix/lamb2-checksrc.html
----------------
* checking R code for possible problems ... NOTE
Warning: non-unique value when setting 'row.names': ?new?
Error in
2011 Apr 14
0
extract p-value from mixed model in kinship package
Dear R experts
I was using kinship package to fit mixed model with kinship matrix.
The package looks like lme4, but I could find a way to extract p-value
out of it. I need to extract is as I need to analyse large number of
variables (> 10000).
Please help me:
require(kinship)
Generating random example data
id <- 1:100
dadid <- c(rep(0, 5), rep(1, 5), rep(3, 5), rep(5, 5), rep(7,
2009 Nov 06
1
Qtl - package - Question
Dear R-Helpers,
I am using qtl package to analyze qtl data from QTL cartographer.
I have the map file and cro file from QTL cartographer. I was trying to
import these two files in R using qtl package.
data=read.cross("qtlcart", ".", "crofile.txt", "mapfile.txt") ### I have
matched the file structure with the one on the website of qtl package - It
matches
2011 Jan 03
0
Using PCA to correct p-values from snpMatrix
Hi R-help folks,
I have been doing some single SNP association work using snpMatrix. This works
well, but produces a lot of false positives, because of population structure in
my data. I would like to correct the p-values (which snpMatrix gives me) for
population structure, possibly using principle component analysis (PCA).
My data is complicated, so here's a simple example of what
2011 Oct 22
3
Sweave, cairo_pdf, CJK, ghostscript
I have had some fun in the last few days trying to put together an annotated map of China with R and some public GIS data:
http://sourceforge.net/projects/outmodedbonsai/files/snpMatrix%20next/1.17.7.11/China_Choropleth_Maps.pdf/download
It is done, and rather nice... there are a few issues:
- the default pdf() device cannot do CJK with embedded fonts - and cairo_pdf() is not hooked up to
2004 Mar 13
1
Installing ncdf package
Hi
I used the command
R CMD INSTALL ncdf
to install ncdf package in linux. Can somebody explain to me what might
be wrong. Thanks. Below is the error.
* Installing *source* package 'ncdf' ...
Special note:
checking for gcc... gcc
checking for C compiler default output... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for
2001 Jan 24
5
trouble with netCDF (PR#824)
Having trouble with netCDF since I upgraded to 1.2.1 (did directly
from 1.1.1). Package was recompiled after the upgrade.
Symptoms:
open.netCDF returns cleanly, but read.netCDF causes R to segfault
and dump core. What else do you need me to write to help?
--please do not edit the information below--
Version:
platform = i586-pc-linux-gnu
arch = i586
os = linux-gnu
system = i586, linux-gnu
2006 Dec 18
1
Memory problem on a linux cluster using a large data set
Hello,
I have a large data set 320.000 rows and 1000 columns. All the data has the values 0,1,2.
I wrote a script to remove all the rows with more than 46 missing values. This works perfect on a smaller dataset. But the problem arises when I try to run it on the larger data set I get an error “cannot allocate vector size 1240 kb”. I’ve searched through previous posts and found out that it might
2008 Dec 23
1
NetCDF within R: installation assistance
Greetings. I am attempting to add NetCDF libraries within R, and have
failed. We have R version 2.8, and are running on a 64-bit Redhat Linux
2.6.18 kernel:
Red Hat Enterprise Linux Client release 5.2 (Tikanga)
Linux halfmoon.ncdc.noaa.gov 2.6.18-92.1.22.el5 #1 SMP Fri Dec 5
09:28:22 EST 2008 x86_64 x86_64 x86_64 GNU/Linux
I have run the installation instructions found at
2011 Oct 27
3
2 x 3 Probability under the null
I have a 2 x 3 matrix called snp and I want to compute the following
probability:
choose(sum(snp[,1]), snp[1,1]) * choose(sum(snp[,2]), snp[1,2]) *
choose(sum(snp[,3]), snp[1,3])/choose(sum(snp), sum(snp[1,]))
but I keep getting Infs and NaNs. Is there a function that can do this in R?
--
Thanks,
Jim.
[[alternative HTML version deleted]]
2012 Aug 28
4
[ncdf4] error converting GEIA data to netCDF
summary: I can successfully ncvar_put(...) data to a file, but when I
try to ncvar_get(...) the same data, I get
> Error in if (nc$var[[li]]$hasAddOffset) addOffset = nc$var[[li]]$addOffset else addOffset = 0 :
> argument is of length zero
How to fix or debug?
details:
R code @
https://github.com/TomRoche/GEIA_to_NetCDF
successfully (if crudely) uses R packages={ncdf4, maps, fields}
2007 Jan 21
2
efficient code. how to reduce running time?
Hi,
I am new to R.
and even though I've made my code to run and do what it needs to .
It is taking forever and I can't use it like this.
I was wondering if you could help me find ways to fix the code to run
faster.
Here are my codes..
the data set is a bunch of 0s and 1s in a data.frame.
What I am doing is this.
I pick a column and make up a new column Y with values associated with that
2006 Apr 26
2
help in R
Hi,
I cant understand where I am going wrong.Below is my code.I would really appreciate your help.
Thanks.
> genfile<-read.table("c:/tina/phd/bs871/hw/genfile.txt",skip=1)
>
> #read in SNP data
> snp.dat <- as.matrix(genfile)
> snp.name <- scan("c:/tina/phd/bs871/hw/genfile.txt",nline=1,what="character")
Read 100 items
2004 Apr 06
2
A package to read and write NetCDF?
I am looking for a package to read and write NetCDF files.
NetCDF package says it can only read, not write.
Another package for the standard binary file format?
Daehyok Shin
2013 Jan 03
4
Index out SNP position
Dear R experts,
I have 2 matix: A& B. I am trying to index B against A - (1) find out B rows that fall between the col 1 and 2 of A& put them into a new vector SNP.I made code as below, but I cannot think of a right way to do it. Could anyone help me with the code? Thanks,Jiang----
A <-
2009 Jul 26
1
splitting multiple data in one column into multiple rows with one entry per column
Dear R colleagues,
I annotated a list of single nuclotide polymorphiosms (SNP) with the
corresponding genes using biomaRt. The result is the following
data.frame (pasted from R):
snp ensembl_gene_id
1 rs8032583
2 rs1071600 ENSG00000101605
3 rs13406898 ENSG00000167165
4 rs7030479
2007 Jan 10
1
Fw: Memory problem on a linux cluster using a large data set [Broadcast]
Hi
I listened to all your advise and ran my data on a computer with a 64 bits procesor but i still get the same error saying "it cannot allocate a vector of that size 1240 kb" . I don't want to cut my data in smaller pieces because we are looking at interaction. So are there any other options for me to try out or should i wait for the development of more advanced computers!
2008 Feb 28
1
Errors melt()ing data...
Hi,
I'm trying to melt() some data for subsequent cast()ing and am
encoutering errors.
The overall process requires a couple of casts()s and melt()s.
########Start Session 1##########
## I have the data in a (fully) melted format and can cast it fine...
> norm1[1:10,]
Pool SNP Sample.Name variable value
1 1 rs1045485 CA0092 Height.1 0.003488853
2 1 rs1045485
2003 Nov 20
2
netCDF, ncdf library
Dear all,
I would like to use data in .netcdf format and for those I have to use
the netCDF or ncdf packages.
Problem : these packages don't seem to work :
"Error in testRversion(descfields) : This package has not been
installed properly
See the Note in ?library" (with netCDF package)
Does anybody have the same problems with these packages ?
Is there any