Displaying 20 results from an estimated 1100 matches similar to: "Paste a matrix column in pairwise fashion with other columns?"
2007 Oct 02
1
Trouble obtaining results from a loop
#Hello,
#I have a question about obtaining results from a loop I have written.
#Below is a sample of individual genotypes from a genetic question I am
working on called "P.genotype.sample ".
P.genotype.sample<-matrix(10,10,10)
P.genotype.sample[,1]<-c(2,2,1,5,1,1,5,6,1,3)
P.genotype.sample[,2]<-c(6,3,3,6,8,1,6,7,2,3)
P.genotype.sample[,3]<-c(2,2,2,3,3,2,2,2,3,3)
2007 Oct 19
1
conduct pairwise column comparisons without comparing a column to itself
# Hello
# I have a question regarding pairwise calculations of a matrix using a
"for-loop."
# Below I have a matrix "X" with 8 columns. These are genotypic data so
Column1 & Column2 is
# a unit, Column3 & Column4 is a unit, Column5 & Column6 is a unit, and
Coulmn7 & 8 is a unit.
# I have a loop designed to calculate the number of times an individual in
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 )
2006 Feb 15
1
no convergence using lme
Hi. I was wondering if anyone might have some suggestions about how I can
overcome a problem of "iteration limit reached without convergence" when
fitting a mixed effects model.
In this study:
Outcome is a measure of heart action
Age is continuous (in weeks)
Gender is Male or Female (0 or 1)
Genotype is Wild type or knockout (0 or 1)
Animal is the Animal ID as a factor
2007 Oct 19
1
(no subject)
# Hello
# I have a question regarding pairwise calculations of a matrix using a
"for-loop."
# Below I have a matrix "X" with 8 columns. These are Genotypic data so
Column1 & Column2 is
# a unit, Column3 & Column4 is a unit, Column5 & Column6 is a unit, and
Coulmn7 & 8 is a unit.
# I have a loop designed to calculate the number of times an individual in
2010 Oct 09
1
question related to multiple regression
Hi,
I am conducting an association analysis of genotype and a phenotype such as
cholesterol level as an outcome and the genotype as a regressor using
multiple linear regression. There are 3 possibilities for the genotype AA,
AG, GG. There are 5 people with the AA genotype, 100 with the AG genotype
and 900 with the GG genotype. I coded GG genotype as 1, AG as 2 and AA as 3
and the p-value for the
2008 Aug 20
4
Looping over groups
Hello,
My R skills are somewhere between novice and intermediary, and I am hoping that some of you very helpful forum members, whom I've seen work your magic on other peoples' problems/questions, can help me here.
I have a matrix with the following format:
(i) individual plants comprising many different genotype groups (i.e., a plant is genotype 1 or genotype 2 or genotype 3, etc). The
2011 Mar 08
1
NaNs in Nested Mixed Model
Dear R users,
I have a problem with something called "NaNs" in a nested mixed model.
The background is that I have studied the number of insect nymphs
emerging from replicated Willow genotypes in the field. I have 15
replicates each of 4 Willow genotypes belonging two 2 Willow species.
Now I want to elucidate the effect of Willow genotype on the number of
emerging nymphs. Previously I
2005 Apr 21
2
ANOVA model
Hi,
Could someone tell me if this is the correct model syntax for the
following dataset:
lme(height~treatment+genotype+treatment*genotype,drought,random=~genotyp
e)
The dataset has two factors: one fixed - treatment, and one random -
genotype. I need to test the effect of both factors to identify their
significance. There are multiple (but not equal) replicates at each
level of genotype (the
2005 Jun 30
1
FW: plot legend outside the grid
-----Original Message-----
From: Ghosh, Sandeep
Sent: Thursday, June 30, 2005 5:43 PM
To: 'Berton Gunter'
Subject: plot legend outside the grid
Thanks for the pointers... I managed to get everything to look and feel the way I want except for the legend to plot outside the grid... Thanks for the note on the par, but I'm not able to it to plot outside the plot grid..
dataFrame <-
2003 Apr 08
2
Basic LME
Hello R Users,
I am investigating the basic use of the LME function, using the following example;
Response is Weight, covariate is Age, random factor is Genotype
model.lme <- lme (Weight~Age, random=~ 1|Genotype)
After summary(model.lme), I find that the estimate of Age is 0.098 with p=0.758.
I am comparing the above model with the AOV function;
model.aov <- aov (Weight~Age + Genotype)
2004 Nov 21
1
Two factor ANOVA in lme
I want to specify a two-factor model in lme, which should be easy?
Here's what I have:
factor 1 - treatment FIXED (two levels)
factor 2 - genotype RANDOM (160 genotypes in total)
I need a model that tells me whether the treatment, genotype and
interaction terms are significant. I have been reading 'Mixed effects
models in S' but in all examples the random factor is not in the main
2003 May 22
3
How to avoid function masking
Hi All,
I've been working on updating the 'genetics' package. As a consequence of
the upgrade, .First.lib() looks like:
.First.lib <- function(libname, pkgname)
{
if (!require(combinat))
warning("Unable to load 'combinat' library. Function
`diseq.ci' will fail.")
require(gregmisc)
genotype <-
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,
2013 Oct 14
1
R Help-how to use sapply w/tapply
Hi,
(Please use ?dput() to share the example dataset. Avoid using images to show dataset. Also, please read the posting guide esp. regarding home work, assignments etc.)
res <- sapply(Gene[,-1],function(x) tapply(x,list(Gene$Genotype),mean))
#or
res2 <-? aggregate(.~Genotype, data=Gene,mean)
#or
library(plyr)
?res3 <- ddply(Gene,.(Genotype),numcolwise(mean))
identical(res2,res3)
2012 Nov 03
2
reorder() in the latticeExtra library
Hello all, thanks for your time and help. Below are my commands, and it
generates a really nice plot, however I am not happy with the reorder()
function. I would like the order to be the same as they appear in the
genotype variable "genotype <- c("CJ1450 NW 4/25/12","CJ1450 BAL
4/25/12","CJ1450 NW 4/27/12","CJ1450 BAL 4/27/12","CJ1721 NW
2010 Sep 03
3
define colors for groups in lattice xyplot
Dear all,
Lattice provides automatic coloring for subgroups on each panel by the
simple use of a groups statement. For an application I want to change
these colors to a predifined set. This works well using a panel function
in stead of the default as long as there are only points in the graphs.
When I set type="b" things get messed up. Any idea why? I include sample
code for
2005 Jun 28
3
Help with stripplot
For the following code is there a way to make the jitter all line up horizontally, instead of them being just randomly spread around a value. So for ex if there are multiple values at 63 for genotype wt then all the values should be plotted on the same y value of 63 but spaced apart by a certain factor or noise..
library(lattice);
dataFrame <- as.data.frame(t(structure(c(
64,'wt',
2012 Feb 20
2
Help on lattice barchart ploting
Hi friends,
I have following data and would like to plot this with barchart() availble
with lattice package.
RsID Freqs Genotype
AAA 63.636 1/1
AAA 32.727 1/2
AAA 3.636 2/2
BBB 85.965 2/2
BBB 14.035 2/1
CCC 63.158 1/1
CCC 21.053 1/2
CCC 15.789 2/2
DDD 26.786 2/2
DDD 46.429 2/1
DDD 26.786 1/1
EEE 32.759 2/2
EEE 43.103 2/1
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