Hi Bogdan,
If you want something like this:
22M 17M 11M
AEBP1 SNV SNV NA
ATR INDEL NA NA
ATR SNV NA NA
BTK NA NA SNV
BTK NA NA INDEL
You're in trouble with repeated row names. Same with column names if
you add extra columns for repeated values. You'll have to change
something in order to make this consistent.
Jim
On Mon, Jul 3, 2017 at 5:22 PM, Bogdan Tanasa <tan...@gmail.com> wrote:
> Dear all,
>
> I would appreciate please a piece of help regarding the use of acast/dcast
> functions in reshape2 package.
>
> Specifically, I'm working with a data frame, that has information about
> SAMPLE, GENE, and TYPE of MUTATION (as shown below):
>
> Sample Gene Type
> 22M AEBP1 SNV
> 17M AEBP1 SNV
> 22M ATR INDEL
> 22M ATR SNV
> 11M BTK SNV
> 11M BTK INDEL
>
>
> I would like to transform this DATAFRAME into a MATRIX that has GENE on
> ROWS, SAMPLE on COLUMNS, and the elements of the matrix are SNV or INDEL
> (ie the types of mutations).
>
> The R code starts with :
>
> y <- data.frame(Sample = x$Sample, Gene = x$Gene, Type=x$Type)
>
> z <- acast(y, Cancer_Gene ~ Sample)
>
> although in z, I do not have the information on Type (i.e.SNV or INDEL).
>
> thanks a lot,
>
> -- bogdan
>
> [[alternative HTML version deleted]]
>
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