Displaying 20 results from an estimated 1000 matches similar to: "Index out SNP position"
2013 Jan 04
0
FW: Index out SNP position
I think you mean between column 1 and 2 of A? Why is 36003918 not
included? It is clearly between 35838396 and 36151202 in the first row of A.
My earlier solution should work fine. Just create a new matrix AX that has
the columns switched so that the start is always column 1 and use that to
identify the ones you want to select. That way you are not modifying B. This
will be faster than checking
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.
2003 Oct 19
1
jail + devfs + snp problem (FreeBSD 5.1-RELEASE-p10)
shell# /sbin/devfs rule -s 2 delset
shell# /sbin/devfs rule -s 2 add hide
shell# /sbin/devfs rule -s 2 add path random unhide
shell# /sbin/devfs rule -s 2 add path urandom unhide
shell# /sbin/devfs rule -s 2 add path zero unhide
shell# /sbin/devfs rule -s 2 add path pty\* unhide
shell# /sbin/devfs rule -s 2 add path pty\* unhide
shell# /sbin/devfs rule -s 2 add path tty\* unhide
shell#
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
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?
--
View this message in context:
2006 Jun 05
3
Fastest way to do HWE.exact test on 100K SNP data?
Hi everyone,
I'm using the function 'HWE.exact' of 'genetics' package to compute p-values of
the HWE test. My data set consists of ~600 subjects (cases and controls) typed
at ~ 10K SNP markers; the test is applied separately to cases and controls. The
genotypes are stored in a list of 'genotype' objects, all.geno, and p-values are
calculated inside the loop over all
2012 Apr 23
2
Overlay Gene Expression on SNP (copy number) data
Hello,
Can anyone please suggest any packages in R that can be used to overlay gene expression data on SNP (affymetrix) copy number ?
Thanks,
Ekta
Senior Research Associate
Bioinformatics Department
Jubilant Biosys Pvt Ltd,
#96, Industrial Suburb, 2nd Stage
Yeshwantpur, Bangalore 560 022
Ph No : +91-80-66628346
The information contained in this electronic message and in any attachments to this
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
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
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
2012 Sep 26
3
replace string values with numbers
Hi everyone, I have a data frame Gene with SNPs eg. P1 P2 P3
CG CG GG
-- -- AC
-- AC CC
AC -- AC I tried to replace all the GG with a value 3. Gene[Gene=="GG"]<-3 It always give me: Warning in `[<-.factor`(`*tmp*`, thisvar, value = 3) :
invalid factor level, NAs generated Does any know if there is anything wrong with my code? Thanks, Zhengyu
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,
2011 Apr 06
5
Need a more efficient way to implement this type of logic in R
I have cobbled together the following logic. It works but is very
slow. I'm sure that there must be a better r-specific way to implement
this kind of thing, but have been unable to find/understand one. Any
help would be appreciated.
hh.sub <- households[c("HOUSEID","HHFAMINC")]
for (indx in 1:length(hh.sub$HOUSEID)) {
if ((hh.sub$HHFAMINC[indx] == '01')
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
2013 Feb 21
3
Ask for help: find corresponding elements between matrix
Dear R experts,
I have two matrix (seq & mat) & I want to retrieve in a new matrix all the numbers from mat that =1 (corresponding to the same row/ column position) in seq, or all the numbers in mat that =-1 in seq. - Replace all the numbers with NA if it's not 1/-1 in seq. There are some "NA"s in seq.
seq=matrix(c(1,-1,0,1,1,-1,0,0,-1,1,1,NA),3,4)
2013 Mar 22
3
Distance calculation
Hi Elisa,
I hope this is what you wanted.
dat1<-read.csv("peaks.csv",sep=",")
#Subset
dat2<-dat1[1:5,]
res1<-do.call(cbind,lapply(seq_len(nrow(dat2)),function(i) do.call(rbind,lapply(split(rbind(dat2[i,],dat2[-i,]),1:nrow(rbind(dat2[i,],dat2[-i,]))), function(x) {x1<-rbind(dat2[i,],x);
2012 Mar 16
3
Faster way to implement this search?
I am working on a simulation where I need to count the number of matches
for an arbitrary pattern in a large sequence of binomial factors. My
current code is
for(indx in 1:(length(bin.05)-3))
if ((bin.05[indx] == test.pattern[1]) && (bin.05[indx+1] ==
test.pattern[2]) && (bin.05[indx+2] == test.pattern[3]))
return.values$count.match.pattern[1] =
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
2012 Jul 05
2
vector entry in matix
hi,
i'm trying to figure out if there's any possibility to write a whole vector
into a matrix or data.frame or something like that. i don't mean
transormation. Here an example:
[,1] [,2]
[1,] "a" "d"
[2,] "b" "e"
[3,] "c" "f"
where e.g. a is a<-c(0,1) vector of length 2, b a vector of length 4,... (i
know that
2011 Jan 23
1
SNP IMPUTATION
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 1 -1
I need to male