Displaying 20 results from an estimated 100 matches similar to: "SNP IMPUTATION"
2011 Jan 22
1
R TABELS
Hi
ihave one table that look like
SNP1 SNP2 SNP3 SNP4 SNP5
SIRE1 1 -1 -1 1 -1
SIRE2 1 -1 1 1 1
SIRE3 -1 -1 1 1 0
SIRE4 -1 1 1 0 1
SIRE5 -1 1 -1 -1 1
SIRE6 0 0 0 1 -1
SIRE7 -1 0 -1 1 1
SIRE8 1 -1 NA 0 NA
SIRE9 -1 1 1 -1 -1
SIRE10 1 1 1 1 1
table 2 only one line
SNP1 SNP2 SNP3 SNP4 SNP5
SIRE100 -1 -1 1
2011 Mar 10
1
snp-chip table
Dear R helpers
I have a table and i need to make new table
table1:
sire snp1 snp2 snp3 snp4 snp5 snp6 snp7 snp8 snp9 snp10
snp11 snp12 snp13 snp14 snp15 8877 -1 -1 -1 -1 0 0 -1 -1 -1 0 1 1 1 -1 -1
7765 1 1 1 0 0 0 -1 1 1 1 0 0 0 1 0 8766 1 1 -1 0 -1 -1 0 -1 0 -1 -1 -1 0 1
0 6756 0 1 0 -1 1 -1 -1 0 0 0 0 -1 0 1 1 5644 -1 0 1 -1 0 0 0 0 -1 -1 0 0 0
0 1
I have table2
sire
2009 Feb 27
5
Filtering a dataset's columns by another dataset's column names
Hello all,
I hope some of you can come to my rescue, yet again.
I have two genetic datasets, and I want one of the datasets to have only the columns that are in common with the other dataset.
Here is a toy example (my real datasets have hundreds of columns):
Dataset 1:
Individual SNP1 SNP2 SNP3 SNP4 SNP5
1 A G T C A
2 T C A G T
3 A C T
2009 Apr 22
3
Merging data frames, or one column/vector with a data frame filling out empty rows with NA's
Hello
I have two data frames, SNP4 and SNP1:
> head(SNP4)
Animal Marker Y
3213 194073197 P1001 0.021088
1295 194073197 P1002 0.021088
915 194073197 P1004 0.021088
2833 194073197 P1005 0.021088
1487 194073197 P1006 0.021088
1885 194073197 P1007 0.021088
> head(SNP1)
Animal Marker x
3213 194073197 P1001 2
1295 194073197 P1002 1
915 194073197
2009 Sep 01
1
permutation and reshuffling
Hi,
I'm looking for an efficient code that will enable me to reshuffle data
(phenotype) for certain number of individuals and creating a loop that will
randomly simulate it for 10000 times *(permutation)*. I also need to find
how I keep the information (p value for each SNP) gathered for all the 10000
iterations.
My data set looks like this (n=500):
Individual #
Phenotype
SNP1
SNP2
2013 Jul 02
2
Recoding variables based on reference values in data frame
I'm new to R (previously used SAS primarily) and I have a genetics data
frame consisting of genotypes for each of 300+ subjects (ID1, ID2, ID3,
...) at 3000+ genetic locations (SNP1, SNP2, SNP3...). A small subset of
the data is shown below:
SNP_ID SNP1 SNP2 SNP3 SNP4 Maj_Allele C G C A Min_Allele T A T G ID1
CC GG CT AA ID2 CC GG CC AA ID3 CC GG
nc
AA
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 Jul 27
1
SNP Tables
Hello,
I have indicators for the present of absent of a snps in columns and the
categorey (case control column). I would like to extract ONLY the tables and
the indices (SNPS) that give me 2 x 3 tables. Some gives 2x 2 tables when
one of the allelle is missing. The data look like the matrix snpmat below:
so the first snp should give me the following table: (aa=0, Aa=1 and AA=2)
aa
2010 Aug 05
2
a question about 'read.table' with or without 'read.table'.(urgent)
Hi, I've got a quite tricky question.
I have a txt file, named 'temp.txt', as the following:
snp1 snp2 snp3
AA 00 00
GG GG 00
00 AA 00
I want to read the file into R.
1) when I use 'read.table' without 'header=T' option,
> temp <- read.table('temp.txt')
# I got
> temp
V1
2009 Mar 26
4
same value in column-->delete
Hi Readers,
I have a question.
I have a large dataset and want to throw away columns that have the same
value in the column itself and I want to know which column this was.
For example
> x<-data.frame(id=c(1,2,3), snp1=c("A","G",
"G"),snp2=c("G","G","G"),snp3=c("G","G","A"))
2009 Mar 20
1
reshape dataframe
Hi,
I have a large dataset on which I would like to do the following:
x<-data.frame(id=c(1,2,3), snp1=c("AA","GG",
"AG"),snp2=c("GG","AG","GG"),snp3=c("GG","AG","AA"))
> x
id snp1 snp2 snp3
1 1 AA GG GG
2 2 GG AG AG
3 3 AG GG AA
And then
2010 Aug 05
2
questions about string handling
Hi, I have a question about the data handling. I have a dataset as following:
ID snp1 snp2 snp3
1001 0/0 1/1 1/1
1002 2/2 3/3 1/1
1003 4/4 3/3 2/2
I want to convert the dataset to the following format:
ID snp1 snp2 snp3
1001 00 AA AA
1002 GG
2011 Dec 13
0
snpStats imputed SNP probabilities
Hi,
Does anybody know how to obtain the imputed SNP genotype probabilities from the snpStats package?
I am interested in using an imputation method implemented in R to be further used in a simulation study context.
I have found the snpStats package that seems to contain suitable functions to do so.
As far as I could find out from the package vignette examples and its help, it gives the
2011 Sep 26
1
Packages for snp, CNV data
Hi,
In addition to GADA, what are the available package in R and bioconductor to analyze amplification, deletion, LOH and indels of CNV, SNP data? Any reference is welcome.
Best,
Carol
2007 May 25
1
Read in 250K snp chips
I'm having trouble getting summaries out of the 250K snp chips in R. I'm
using the oligo package and when I attempt to create the necessary SnpQSet
object (to get genotype calls and intensities) using snprma, I encounter
memory issues.
Anyone have an alternative package or workaround for these large snp chips?
--
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2007 Oct 30
0
Plotting question: how to plot SNP location data?
Hello,
I would like to plot specific SNPs with their exact locations on a
chromosome. Based on my genotyping results I would like to separate
these SNPs in three different categories: 1, 2 and 3 and use different
colours to represent these categories. The script below generates the
sample data. I can plot these with the image function using the
following:
val <- 1:3
samp <- sample(val,
2009 Feb 09
0
Generating missingness on SNP data
Dear all,
I generated a dataset with 500 unrelated individuals and 10 biallelic
SNPs. From this dataset,I would like to create data with 5% missingness on
genotype information at random and also data with 5% genotyping error.
Can someone help me with how I can do it.
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2023 Aug 28
1
SEV, SEV-ES, SEV-SNP
When SEV is enabled in domcapabilities does that just mean any of SEV,
SEV-ES, SEV-SNP is possible on the hardware?
Similarly, does enabling SEV as a launchSecurity option in a domainXML mean
that whichever SEV is available will be enabled? And if the guest policy
has the ES flag set, it will not be created unless ES is enabled?
Sorry if these questions don't make sense or are ill-formed.
2009 Jan 28
1
Character SNP data to binary MAF data
Hi
I am sure there is a function out there already but I couldn't find it.
I have SNP data, that is, a matrix which contains in each row two
characters (they are different in each row) and I would like to
convert this matrix to a binary one according to the minor allele
frequency. For non-geneticists: I want to have a binary matrix
for which in each row the 0 stands for the less frequent
2008 Aug 21
0
Need Functional SAP APO DP and SNP
Hi ,
This is prabhu from levanture Inc.
Our Tier1 vendor Needs Functional SAP APO DP and SNP
Location:CA
Duration:6+ Months
Project is undergoing a change in company code for part of its business
within USA. Such a change requires changes to our existing setup in SAP R/3
and SAP APO. The goal is to ensure business as usual post change in company
code for Global Supply Chain Management