Displaying 20 results from an estimated 10000 matches similar to: "Is there any package can be used to solve individual haplotyping problem?"
2010 Nov 09
0
haplotype and epistasis analysis using 3 or more SNPs?
Dear Mme/Mr.
Hope you are doing well. I am doing some genetic analysis using The R software and I have difficulties to find how I can perform an Interaction/epistasis analysis using 3 or more SNPs (=markers) ? (In the instructive manual, there is only an interaction/epistasis analysis with 2 markers).
In addition can you please inform me how I can perform Haplotype analysis and if there is an
2011 Jan 12
0
adonis, amova and haplotype frequency
Dear All,
I'd like to perform adonis (from the vegan package) rather than amova
(in ade4) on some haplotype data, as I have crossed factors. Is there a
simple way to tweak the source to allow weights (haplotype frequencies)
in a similar way to amova?
Best
Simon
2009 Jan 22
1
infer haplotypes phasing trios tdthap
Dear R mailing list,
I have a dataset with genotypes from trios and I would like to infer
haplotypes for each mother, father and child. The package that I could
find that can do this is tdthap.
But when the mother is homozygous (e.g., 2/2) the haplotype is called as
not possible to infer (0); I would prefer for it to call the genotype
(2). From what I understand it is doing what I would like
2017 Oct 27
1
genetics: backward haplotype transmission association algorithm
Dear friends - a couple of papers in PNAS (lastly:framework for making
better predictions by directly estimating variables' predictivity, Lo et
al PNAS 2016; 113:14277-14282) have focused interest on mapping complex
traits to multiple loci spread all over the genome. I have been around
on the relevant taskview(s) I hope but fail to see that the backward
haplotype transmission association
2016 Apr 26
0
Haplotype network appearance
Hi,
I'm doing haplotype networks with the package pegas and the script from
Jimmy O'Donell's blog. The networks which I obtain are a little ugly and
I'd like to change some aspects of their appearance, but I'm just starting
with R and I don't know how to do it. I have the following problems:
-Some nodes overlap. I increase the scale.ratio but then I get a tiny
legend. So
2006 Mar 24
1
cox model for haplotypes
Hi,
Anybody knows a function that can fit haplotype data to a Cox model.
I've been searching it in the web without succeed.
I use "haplo.stats" package, but unfortunatelly it's not possible to
analyse survival data, amb I right?.
Thanks in advance.
Isaac Subirana (isubirana@imim.es)
[[alternative HTML version deleted]]
2006 Apr 18
0
Version 1.0 of hapassoc now available from CRAN
Version 1.0 of hapassoc now available from CRAN
hapassoc is an R package for likelihood inference of trait associations
with SNP haplotypes and other attributes using the EM Algorithm. Recent
changes include the addition of anova and logLik methods for the
class hapassoc, to allow users to perform likelihood ratio tests of
haplotype effects. Other changes include bug-fixes and improvements to
2006 Apr 18
0
Version 1.0 of hapassoc now available from CRAN
Version 1.0 of hapassoc now available from CRAN
hapassoc is an R package for likelihood inference of trait associations
with SNP haplotypes and other attributes using the EM Algorithm. Recent
changes include the addition of anova and logLik methods for the
class hapassoc, to allow users to perform likelihood ratio tests of
haplotype effects. Other changes include bug-fixes and improvements to
2007 May 25
1
Speeding up resampling of rows from a large matrix
I'm trying to:
Resample with replacement pairs of distinct rows from a 120 x 65,000
matrix H of 0's and 1's. For each resampled pair sum the resulting 2
x 65,000 matrix by column:
0 1 0 1 ...
+
0 0 1 1 ...
_______
= 0 1 1 2 ...
For each column accumulate the number of 0's, 1's and 2's over the
resamples to obtain a 3 x 65,000 matrix G.
For those
2012 Oct 23
1
factor or character
Hi,
The program below work very well.
(snps = c('rs621782_G', 'rs8087639_G', 'rs8094221_T', 'rs7227515_A',
'rs537202_C'))
Selec = todos[ , colnames(todos) %in% snps]
head(Selec)
But, I have a data set with 1.000 columns and I need extract 70 to use
(like snps in command above).
This 70 snps are in a file. So I create a file to extract them with
2012 Aug 24
0
A question about GRAMMAR calculations in the FAM_MDR algorithm
Dear R developers:
I am a PHD candidate student in the school of public health of Peking
University and my major is genetic epidemiology. I am learning the FAM-MDR
algorithm, which is used to detect the gene-gene and gene-environment
interactions in the data of pedigree. The codes were written by Tom
Cattaert of the University of Liege. The algorithms and the sample datasets
are available at
2012 Mar 14
3
Needing a better solution to a lookup problem.
I have a solution (actually a few) to this problem, but none are computationally efficient enough to be useful. I'm hoping someone can enlighten me to a better solution.
I have data frame of chromosome/position pairs (along with other data for the location). For each pair I need to determine if it is with in a given data frame of ranges. I need to keep only the pairs that are within any of
2014 Jul 21
1
Multiple versions of data in a package
Dear R-devel,
I am writing for help on how I should include parallel sets of data in
my package.
Brief summary: I am new to using data within packages. I want a user to
be able to specify one of two alternative versions of within-package
datasets to use, and I want to load just that one. I have a solution
that works, but it doesn't seem as simple as it should be from a user's
2011 Apr 18
2
Working with massive matrices in R
Hello,
I'm (eventually) attempting a singular value decomposition of a 3200 x
527829 matrix in R version 2.10.1. The script is as follows:
###---------Begin Script here-------###
library(Matrix)
snps <- 527829 ## Number of SNPs
N <- 3200 ## Sample size
y <- rnorm(N, 100,1) ## simulated phenotype
system.time(
## read in matrix
2008 Sep 19
2
Extract method for a new class
Dear list,
I am trying to write a package for simulating meioses in R. We defined a class 'haplotype' which contains the basic units of our simulation:
setClass("haplotype",representation(snp = "numeric",qtl = "list",
hID = "numeric",phID0 = "numeric",phID1 = "numeric"),
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
2005 Mar 04
0
Is aggregate() what I need here?
I'm pretty new to R, and I've been given a script by a user who wants
some help with it. I know enough about the way R works to know that
this is a very inefficient way to do what the user wants (the
LSB_JOBINDEX stuff is added by me so that this can work on many
hundreds of input data files as LSF jobs - it's the nested loops I'm
really interested in):
2004 Feb 19
1
piece wise application of functions
Dear all,
After struggling for some time with *apply() and eva() without
success, I decided to ask for help.
I have 3 lists labeled with, each contains 3 different
interpolation functions with identical names:
> names(missgp0)
[1] "spl.1mb" "spl.2mb" "spl.5mb"
>
> names(missgp1)
[1] "spl.1mb" "spl.2mb" "spl.5mb"
>
>
2005 Apr 13
1
logistic regression weights problem
Hi All,
I have a problem with weighted logistic regression. I have a number of
SNPs and a case/control scenario, but not all genotypes are as
"guaranteed" as others, so I am using weights to downsample the
importance of individuals whose genotype has been heavily "inferred".
My data is quite big, but with a dummy example:
> status <- c(1,1,1,0,0)
> SNPs <-
2013 Nov 08
1
SNPRelate: Plink conversion
Hi,
Following my earlier posts about having problems performing a PCA, I have
worked out what the problem is. The problem lies within the PLINK to gds
conversion.
It seems as though the SNPs are imported as "samples" and in turn, the
samples are recognised as SNPs:
>snpsgdsSummary("chr2L")
Some values of snp.position are invalid (should be > 0)!
Some values of