How to select values based on specific condition from the matrix in R

Question: How to select values based on specific condition from the matrix in R

4.8 years ago by

MAPK • 1.5k

United States

MAPK • 1.5k wrote:

Hi Guys,

I have a large matrix as shown below mymatrix. I would like to know if there is any way I can get the result in the form of list or matrix for each position with only those nucleotides that have values( i.e ones without NA's) and in decreasing order. For example, I want to get the result in these format:

In the form of matrix:

pos 161111 T(17) C(1)

pos 99022222 G(24) A(3)

or in the form of list

pos161111

T C

17 1

pos 99022222

G A

24 3

and so forth...Thank you.

mymatrix

`pos`	`A`	`C`	`G`	`T`	`N`
`1611111`	`NA`	`1`	`NA`	`17`	`NA`
`99022222`	`3`	`NA`	`24`	`NA`	`NA`
`99092333`	`NA`	`5`	`NA`	`91`	`NA`
`233232333`	`2`	`22`	`NA`	`NA`	`NA`

R • 1.4k views

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modified 4.8 years ago by Steven Lakin • 1.5k • written 4.8 years ago by MAPK • 1.5k

How large of a matrix are we talking here? An efficient solution might be needed if it is too large. Otherwise, this problem is relatively easy and I will answer it when you reply.

ADD REPLY • link written 4.8 years ago by Steven Lakin • 1.5k

It's fairly a large matrix. Thank you!

ADD REPLY • link written 4.8 years ago by MAPK • 1.5k

What dimensions?

dim(mymatrix)

ADD REPLY • link written 4.8 years ago by Steven Lakin • 1.5k

Right now my matrix is of 6023 by 8.

ADD REPLY • link written 4.8 years ago by MAPK • 1.5k

Ok, that's not too bad. I will write a quick answer for it in a sec.

ADD REPLY • link written 4.8 years ago by Steven Lakin • 1.5k

Thank you, I would really appreciate that!

ADD REPLY • link written 4.8 years ago by MAPK • 1.5k

transformMyMatrix <- function(mymatrix, outputFile) { for(i in 1:nrow(mymatrix)) { temp <- paste(c("pos(", mymatrix[i, "pos"], ")"), collapse='') for(j in 2:ncol(mymatrix)) { if(!is.na(mymatrix[i,j])) { temp <- c(temp, paste(c(names(mymatrix)[j], "(", mymatrix[i,j], ")"), collapse='')) } } write.table(t(as.matrix(temp)), file=outputFile, sep="\t", append=T, quote=F, row.names=F, col.names=F) } }

> transformMyMatrix(mymatrix, outputFile="newMatrix.txt") > newMatrix <- read.table(file="newMatrix.txt", sep="\t") > newMatrix V1 V2 V3 1 pos(1611111) C(1) T(17) 2 pos(99022222) A(3) G(24) 3 pos(99092333) C(5) T(91) 4 pos(233232333) A(2) C(22)

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