converting a matrix of gene links to a normal matrix
hi,
sorry i have a list of interaction between my genes like below
from to
AT5G05410 AT2G26150 0.0636682705541425
AT4G34410 AT1G12610 0.055895368934279
AT2G46830 AT1G01060 0.0554920876837871
how i can convert the above file to something like below
AT1G01060 AT1G01170 AT1G01260
AT1G01060 1.00000000 0.3885284 -0.14720327
AT1G01170 0.38852841 1.0000000 -0.29069241
AT1G01260 -0.14720327 -0.2906924 1.00000000
AT1G01380 -0.01865947 0.2699235 0.30973373
AT1G01490 0.24681279 0.3955740 -0.07497821
AT1G01500 0.05720335 -0.1786700 -0.26813919
thank you in advance
1 answer
Untested, please check for minor errors:
my.dimn <- unique(as.character(c(row.matrix[,1], row.matrix[,2] ) ))
### find the appropriate dim names for the matrix, having a matrix with these
### dimnames provides all possible combinations
my.dist <- matrix(NA, nrow=length(dimn), ncol=length(dimn), dimnames=list(my.dimn, my.dimn)) ## make a quadratic matrix of NA
diag(my.dist) <- 1 # diagonale will be 1
my.dist[row.matrix[,1:2]] <- row.matrix[,3] # yes this works, everything not defined in the row matrix is NA
This code converts a sparse matrix in row coordinate notation into a full matrix, see the Matrix package for more options, e.g. sparse matrix.
• 0 views
•
link
updated
by
Ram
•
written
by
Michael Dondrup
•
written
by
Michael Dondrup
Log in to answer this question.
are you sure your input is that data only?
no it is a big matrix but i pasted only a few rows for example, may you tell me the solution please?
How can one know what to do without looking into the complete data (complete rows of a toy set). There is one numerical column in your input data but 3 in expected output.