May 2014, francesca casalino wrote:
I am having this problem because I need to run a meta-analysis and to
align
all the variants between the different studies included in the
meta-analysis I need to know the effect allele used to get the beta (so
that I can flip the beta if the effect allele
But then how do you know which allele is the reference and which the risk
allele (between A/T/C/G)?
2014-05-26 1:41 GMT+01:00 David Duffy david.du...@qimr.edu.au:
francesca casalino francy.casal...@gmail.com asked:
Does anyone know how to find the reference allele used for genetic
).
Thanks for your help.
Francesca
2014-05-26 11:13 GMT+01:00 francesca casalino francy.casal...@gmail.com:
But then how do you know which allele is the reference and which the risk
allele (between A/T/C/G)?
2014-05-26 1:41 GMT+01:00 David Duffy david.du...@qimr.edu.au:
francesca casalino
Hi,
Does anyone know how to find the reference allele used for genetic
associations ran in snpStats?
I have ran several associations using snp.rhs.tests, but I cannot tell which
allele was used as the effect allele. Is it the one coded as Al1 in the
SNP.support file? I can find the RAF (risk
Hi,
I am trying to produce a ggplot graph using specific characters in the
labels, but ggplots doesn't seem to support certain symbols.
For example, when I type:
print(\u25E9)
it shows a square which is half black, but when I try to use it in ggplot
it doesn't print.
I am using facet_wrap, but
Dear R experts,
I am trying to arrange multiple plots, creating one graph for each
size1 factor variable in my data frame, and each plot has the median
price on the y-axis and the size2 on the x-axis grouped by clarity:
library(ggplot2)
df - data.frame(price=matrix(sample(1:1000, 100, replace =
, Feb 18, 2013 at 6:04 AM, francesca casalino
francy.casal...@gmail.com wrote:
Dear R experts,
I am trying to arrange multiple plots, creating one graph for each
size1 factor variable in my data frame, and each plot has the median
price on the y-axis and the size2 on the x-axis grouped
I am sorry I have confused you, the logs are all base e:
ln(a) = 1347
ln(b) = 1351
And I am trying to solve this expression:
exp( ln(a) ) - exp( ln(0.1) + ln(b) )
Thank you.
2013/2/4 francesca casalino francy.casal...@gmail.com:
Dear R experts,
I have the logarithms of 2 values:
log
Dear R experts,
I have the logarithms of 2 values:
log(a) = 1347
log(b) = 1351
And I am trying to solve this expression:
exp( ln(a) ) - exp( ln(0.1) + ln(b) )
But of course every time I try to exponentiate the log(a) or log(b)
values I get Inf. Are there any tricks I can use to get a real
Dear R experts,
I have an R script that creates multiple scripts and submits these
simultaneously to a computer cluster, and after all of the multiple
scripts have completed and the output has been written in the
respective folders, I would like to automatically launch another R
script that works
Hi, I am trying to match the order of the rownames of a dataframe with
the rownames of another dataframe (I can't simply sort both sets
because I would have to change the order of many other connected
datasets if I did that): Also, the second dataset (snp.matrix$fam) is
a snp matrix slot:
so for
Dear experts,
I am trying to create a data frame from the residuals I get after
having applied a linear regression to each column of a data frame, but
I don't know how to create this data frame from the resulting list
since the list has differing numbers of rows.
So for example:
age-
Dear R experts,
I have a large database made up of mixed data types (numeric,
character, factor, ordinal factor) with missing values, and I am
looking for a package that would help me impute the missing values
using  either the mean if numerical or the mode if character/factor.
I maybe could use
not be sensible to simply fill missing values by
mean or mode as multiple imputation becomes the norm this day. For
your specific question, na.roughfix in randomForest package would do
the work.
Weidong Gu
On Tue, Oct 11, 2011 at 8:11 AM, francesca casalino
francy.casal...@gmail.com wrote
Thank you very much to both Ken and Peter for the very helpful
explanations.
Just to understand this better (sorry for repeating but I am also new in
statisticsÂ…so please correct me where I am wrong):
Ken' method:
Random sampling of the mean, and then using these means to construct a
Dear Peter and Tim,
Thank you very much for taking the time to explain this to me! It is much
more clear now.
And sorry for using the space here maybe inappropriately, I really hope this
is OK and gets posted, I think it is really important that non-statisticians
like myself get a good idea of
Yes, your code did exactly what I needed.
Thank you!!
-f
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Ok I added quoting and it did work...Not sure why, but thank you for both
your replies!
-f
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Sorry---I thought it worked but I think I am actually definitely doing
something wrong...
The problem might be that there are NA's and there are also duplicated
values...My fault. I can't figure out what is going wrong...
I'll be more thorough and modify the two df to mirror more what I have to
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