Displaying 20 results from an estimated 103 matches for "allelic".
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allele
2003 Sep 04
1
Allelic Differentiation, sampling, unique(), duplicated()
Hi people,
I have made some progress trying to work out how to solve this problem
but I have got a bit stuck - sorry if this turns out to be a simple
exercise . .
Allelic Differentiation (AD) in genetics measures the number of
different alleles between (say) two populations eg:
Organisms in Pop 1 have alleles: a, b, c, d, e
Organisms in Pop 2 have alleles: b, b, c, d, e
Different (unique) alleles (n) are: a
[unique() does not do what I want here for comparing...
2007 Sep 21
1
Help create a loopto conduct multiple pairwise operations
#Hello,
#I have three data frames, X,Y and Z with two columns each and different
numbers of rows.
# creation of data frame X
X.alleles <- c(1,5,6,7,8)
X.Freq <- c(0.35, 0.15, 0.05 , 0.10, 0.35)
Loc1 <- cbind( X.alleles,X.Freq)
X <- data.frame(Loc1)
#creation of data frame Y
Y.alleles <- c(1,4,6,8)
Y.Freq <- c(0.35, 0.35, 0.10, 0.20 )
2007 Mar 16
1
ideas to speed up code: converting a matrix of integers to a matrix of normally distributed values
Hi all,
[this is a bit hard to describe, so if my initial description is
confusing, please try running my code below]
#WHAT I'M TRYING TO DO
I'd appreciate any help in trying to speed up some code. I've written
a script that converts a matrix of integers (usually between 1-10,000
- these represent allele names) into two new matrices of normally
distributed values (representing
2008 Aug 10
1
Scripting - query
I have a vector:
alleles.present<-c("D3", "D16", ... )
The alleles present changes given the case I'm dealing with - i.e. either
all of the alleles I use for my calculations are present, or some of them.
Depending on what alleles are present, I need to make matrices and do
calculations on those alleles present and completely disregard any formula
or other use of the
2008 Apr 19
1
resampling from distributions
Hello All,
Once again thanks for all of the help to date. I am climbing my R learning
curve. I've got a few more questions that I hope I can get some guidance on
though. I am not sure whether the etiquette is to break up multiple
questions or not but I'll keep them together here for now as it may help put
the questions in context despite the fact that the post may get a little
long.
2009 Jan 19
1
Deleting columns where the frequency of values are too disparate
Hello R-help community,
I have another question about filtering datasets.
Please consider the following "toy" data matrix example, called "x" for simplicity. There are 20 different individuals ("ID"), with information about the alleles (A,T, G, C) at six different loci ("Locus1" - "Locus6") for each of these 20 individuals. At any single locus
2002 Nov 27
0
R genetics package now available
The "genetics" package for handling single-locus genetic data is now
available on CRAN in both source and Windows binary formats. The purpose of
this package is to make it easy to create and manipulate genetic
information, and to facility use of this information in statistical models.
The library includes classes and methods for creating, representing, and
manipulating genotypes
2002 Nov 27
0
R genetics package now available
The "genetics" package for handling single-locus genetic data is now
available on CRAN in both source and Windows binary formats. The purpose of
this package is to make it easy to create and manipulate genetic
information, and to facility use of this information in statistical models.
The library includes classes and methods for creating, representing, and
manipulating genotypes
2007 Aug 30
2
How to multiply all dataframe rows by another dataframe's columns
Hello,
I have two data frames, X and Y, with two columns each and different numbers
of rows.
# creation of data frame X
Loc1.alleles <- c(1,5,6,7,8)
Loc1.Freq <- c(0.35, 0.15, 0.05, 0.10, 0.35)
Loc1 <- cbind( Loc1.alleles,Loc1.Freq)
X <- data.frame(Loc1)
#creation of data frame Y
Loc2.alleles <- c(1,4,6,8)
Loc2.Freq <- c(0.35, 0.35,
2012 May 13
0
how to calculate risk allele or score allele
Hello,
In a case control study how to calculate the risk allele or score allele.
Regards
GRR
[[alternative HTML version deleted]]
2012 Jun 14
1
Can someone recommend a package for SNP cluster analysis of Fluidigm microarrays?
I know that there are quite a few packages out that there for cluster
analysis. The problem that I am facing is finding a package that will not
incorporate all my samples into clusters but just the samples that fit a
threshold (that I have not set yet and may need help finding the right
level) for genotyping. It should be able to "no call" samples outside the
clusters. It also needs to
2005 Jul 07
3
What method I should to use for these data?
Dear R user:
I am studying the allele data of two populations.
the following is the data:
a1 a2 a3 a4 a5 a6 a7 a8 a9
a10 a11 a12 a13 a14 a15 a16 a17
pop1 0.0217 0.0000 0.0109 0.0435 0.0435 0.0000 0.0109 0.0543
0.1739 0.0761 0.1413 0.1522 0.1087 0.0870 0.0435 0.0217 0.0109
pop2 0.0213 0.0213 0.0000 0.0000 0.0000 0.0426 0.1702 0.2128
0.1596 0.1809 0.0957 0.0745 0.0106
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
2011 Dec 09
1
minor allele frequency comparison
Hi all,
We are using two methods to identify SNPs. One is based on resequencing
the genome and aligning the reads to the sequenced genome to identify SNPs
(data available for 44 individuals). Another is based on SNP array with
selected loci (30000 loci, 870 individuals). I want to compare the results
from the resequencing based minor allele frequency and Array based minor
allele frequency.
2010 Mar 26
1
how to read this special form of data
Dear R listers,
I have a data file looks like the following:
Testing marker: s_1
---------------------------------------------
Allele df(0) -LnLk(0) df(T) -LnLk(T) ChiSq p
3 7995 29320.30 7994 29311.85 16.90 4e-05 (2229/8000 probands)
Testing marker: s_2
---------------------------------------------
Allele df(0)
2006 Apr 27
2
Incomplete Trio in TDT analysis
I am involved in a study where, as in most of life, men demonstrate
themselves to be recalcitrant. So while we have many probands and most of
their mothers we only have about 50% of the trios being complete.
I have been running tdt and trio.types. It appears as if it is ignoring the
duos. Sometimes a duo can be informative. For instance
Father ..missing
Mother 1/2
Proband 1/1
This duo shows that
2007 Jun 19
1
genetics package not working
Has something changed in R that requires an update in the genetics package
by Gregory Warnes? I am using R version 2.5.0
This used to work
> summary(founders[,59])
to prove that it is a genotype class
> class(founders[,59])
[1] "genotype" "factor"
Now when I issue the command:
> summary(founders[,59])
I get:
Error in attr(retval, "which") <- which :
2006 May 05
1
How to a handle an error in a loop
I am about one step away from heaven on earth. I think only one step!
I am using dgc.genetics to run a TDT test on thousands of genetic loci. I
have learnt (through the help of others on this mailing list) to send the
complex output to useful data frames which in turn allow me to look at the
big picture and screen the thousands of loci.
Resultdt<-lapply(PGWide[,240:290], tdt)
the above
2006 Dec 29
1
Genotypes are not all the same
I have been merrily using the genetics package and more specifically have
been using the makeGenotypes and genotypes function. I check my
accomplishments by going
> class(g2)
[1] "genotype" "factor"
and likewise
> class(g1)
[1] "genotype" "factor"
Yet when I execute a command such as allele count I get this
> allele.count(g1)
D I
[1,]
2007 Sep 19
0
Create a loop to conduct multiple pairwise binary operations Retry
#Hello,
# Sorry, my last letter contained an error this code should work
#I have three data frames, X,Y and Z with two columns each and different
numbers of rows.
# creation of data frame X
X.alleles <- c(1,5,6,7,8)
X.Freq <- c(0.35, 0.15, 0.05 , 0.10, 0.35)
Loc1 <- cbind( X.alleles,X.Freq)
X <- data.frame(Loc1)
#creation of data frame Y
Y.alleles