2009/1/29 Patrick Aboyoun :
> Hadassa,
> You may want to check out the snpMatrix package in Bioconductor
>
> http://bioconductor.org/packages/2.3/bioc/html/snpMatrix.html
> http://bioconductor.org/packages/2.4/bioc/html/snpMatrix.html
>
> It contains classes that manage this type of information and
Hadassa,
You may want to check out the snpMatrix package in Bioconductor
http://bioconductor.org/packages/2.3/bioc/html/snpMatrix.html
http://bioconductor.org/packages/2.4/bioc/html/snpMatrix.html
It contains classes that manage this type of information and should
minimize your coding effort.
The first step is to convert your data to all uppercase with toupper().
Then it depends on how tidy the data are: are there missing data, are some SNPs
monomorphic in your sample, etc.
If there are no missing data you can use
N<-ncol(the_data)
halfN <- N/2
maf_one_row <-function(arow) {
r
2009/1/29 Hadassa Brunschwig :
> Hi
>
> An example is as follows. Consider the character 3x6 matrix:
>
> a A a T A t
> G g t T T t
> A a C C c c
>
> For each row I would like to identify the most frequent letter and
> assign a 1 to it and 0
> to the less frequent character. That is, in row 1 the mo
Hi
An example is as follows. Consider the character 3x6 matrix:
a A a T A t
G g t T T t
A a C C c c
For each row I would like to identify the most frequent letter and
assign a 1 to it and 0
to the less frequent character. That is, in row 1 the most frequent
letter is A (I do not differentiate be
Hi
I am sure there is a function out there already but I couldn't find it.
I have SNP data, that is, a matrix which contains in each row two
characters (they are different in each row) and I would like to
convert this matrix to a binary one according to the minor allele
frequency. For non-genetici
6 matches
Mail list logo
