Displaying 11 results from an estimated 11 matches for "al1".
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2010 Nov 29
2
FW: how to use by() ?
Thank you for the suggestion, Bill. The result is not quite what I would like. Here's sample code for you or anyone else who may be interested:
Al1 = c('A','C','C','C')
Al2 = c('G','G','G','T')
Freq1 = c(0.0078,0.0567,0.9434,0.9908)
MAF = c(0.0078,0.0567,0.0566,0.0092)
m1 = data.frame(Al1=Al1, Al2=Al2,Freq1=Freq1,MAF=MAF,major_allele='')
m1
Al1 Al2 Freq1 MAF major_a...
2010 Nov 29
3
how to use by() ?
Hello, All!
How might one accomplish this using the by() function?
m1 is a data frame.
# populate column "m1$major_allele"
for ( i in 1:length(m1$major_allele)) {
if ( m1$Freq1[i] == m1$MAF[i]){
m1$major_allele[i] = m1$Al1[i]
}
else{
m1$major_allele[i] = m1$Al2[i]
}
}
Jim
[[alternative HTML version deleted]]
2013 Apr 11
2
group data
Hey,
I have a dataset and I want to identify the records by groups for further
use in ggplot.
Here is a sample data:
ID Value
AL1 1
AL2 2
CA1 3
CA4 4
I want to identify all the records that in the same state (AL1 AND A2),
group them as "AL", and do the same for CA1 and CA4. How can I have an
output like:
ID Value State
AL1 1 AL
AL2 2 AL
CA1 3 CA
CA4 4 CA
Thanks for your help!
[[alte...
2009 Sep 18
1
Incorrect Dimension
...this script above i get the message "Error in gen[j, i] :
incorrect number of dimensions". However gen is 1000x200 (ind x loc) and so
is g
could anybody help me
for (i in 1 : loc) { #loc=200
for (j in 1 : ind) { #ind=1000
g1 <= function ( gen ) matrix ( if (gen[j, i] == 0) al1 [i, 1] + al1 [i, 1]
else if (gen [j, i] == 1) al1 [i, 1] + al2 [i, 1] else if (gen [j,
i] == 2) al2 [i, 1] + al2 [i, 1] else 999, ncol = loc, nrow = ind)
g2 <= function ( gen ) sample (b1, 1, re = T) #b1 is 1x3 and came from a
vector 1000X1 (e.g b1 <- c(x [1000,1]...)
xx <=...
2009 Sep 17
3
How to separate a function by 2 probabilities
Good Mourning,
I have a function to generate a matrix as I show part of it;
g[j,i]<-if (gen[j,i]==0) al1[i,1]+al1[i,1] else ...
However i would like that this function occurred with a probability P and
that another function (another formula to generate g matrix) with
probability P-1
That?s it, if P is .7, i would like that in 70% of the times (for random i
and j) the matrix g was generated according...
2008 Mar 07
3
Combine two columns
Is there a way to combine two columns within a data frame?
Example data:
id snp AL1 AL2
1500 30 A B
1510 30 A A
1520 30 A B
This is what I would like:
indv snp AL1AL2
1500 30 AB
1510 30 AA
1520 30 AB
Any help is greatly appreciated.
Alysta
2010 Dec 09
4
lapply getting names of the list
Hello All,
I have a toy dataframe like this. It has 8 columns separated by tab.
Name SampleID Al1 Al2 X Y R Th
rs191191 A1 A B 0.999 0.09 0.78 0.090
abc928291 A1 B J 0.3838 0.3839 0.028 0.888
abcnab A1 H K 0.3939 0.939 0.3939 0.77
rx82922 B1 J K 0.3838 0.393 0.393 0.0...
2006 Mar 25
1
Trouble phrasing an R command that will run the model i need (ANOVA, nes
...te with respect
to each factor.
Just in the interests of clarifying things as much as possible: one of my
datasets looks like this(apologies if the formatting gets weird):
foresttype region crosstype experiment linelabel yproductivity
l g wx 1 al1
63
l g wx 1 al2
26
... and so on.
Each horizontal line refers to a single observation. The first horizontal
line, for example, refers to a single cross that was found to have a
yproductivity value of "63", and...
2009 Jun 03
1
Would like to add this to example for plotmath. Can you help?
...eetings:
I would like comments on this example and after fixing it up, I need
help from someone who has access to insert this in R's help page for
plotmath.
I uploaded a drawing
http://pj.freefaculty.org/R/Normal-2009.pdf
that is created by the following code
http://pj.freefaculty.org/R/Normal1_2009_plotmathExample.R
This will be a good addition to the plotmath help page/example.
Here's why:
plotmath can be somewhat challenging. A few more concrete examples
of ways in which users can combine values from R programs with
plotmath expressions will be helpful to new users. In partic...
2010 Mar 09
3
Shade area under curve
I want to shade the area under the curve of the standard normal density.
Specifically color to the left of -2 and on. How might i go about doing
this?
Thanks
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2005 Sep 30
0
p-value for non-linear variable in overdispersed glm()
...optim() by first minimising
glm(resp~ var1 + var2, family=binomial, data=data)$deviance
where var1= exp(-a1*dist1), and var2= exp(-a2*dist2), where a1 and a2 are
parameters and dist1 and dist2 are independent variables.
Next, I calculate the value of var1 (and var2) by plugging in the value of
al1 (and al2) that minimises deviance,
and fit glm(resp~ var1+var2 , family=binomial, data=data)
Var1 in this model thus includes two parameters - the standard glm()
coefficient and a1. This is (of course) not recognized by drop1().
Usually I extract a rough p-value for var1 in this model by
1-pchis...