GWAS array to matrix

Question

(this will be a supposition because the number are higher but to make things easier)

Imagine that you have genotyped 10 persons and you have 3 SNIPS each one with 2 alels. then you end up with a matrix like this:

, , 1

	[,1]	[,2]	[,3]	[,4]	[,5]	[,6]	[,7]	[,8]	[,9]	[,10]
[1,]	0	0	0	0	1	1	0	1	0	0
[2,]	0	0	0	1	0	1	0	1	0	0

, , 2

	[,1]	[,2]	[,3]	[,4]	[,5]	[,6]	[,7]	[,8]	[,9]	[,10]
[1,]	1	0	0	0	1	1	0	1	0	0
[2,]	1	0	1	1	0	1	0	1	0	0

, , 3

	[,1]	[,2]	[,3]	[,4]	[,5]	[,6]	[,7]	[,8]	[,9]	[,10]
[1,]	0	0	0	0	0	1	0	1	0	0
[2,]	0	0	0	0	0	1	0	1	0	0

I would transform my array and put: something like:

if there are two 0 on the same column then is a 0.
if there is a 0 and a 1 then is a 1.
if there is a 1 and a 0 then is a 1.
if there are two 1 then is a 2.

I think is more easy to understand with visually.

, , 1

	[,1]	[,2]	[,3]	[,4]	[,5]	[,6]	[,7]	[,8]	[,9]	[,10]
[1,]	0	0	0	1	1	2	0	2	0	0

, , 2

	[,1]	[,2]	[,3]	[,4]	[,5]	[,6]	[,7]	[,8]	[,9]	[,10]
[1,]	2	0	1	1	1	2	0	2	0	0

, , 3

	[,1]	[,2]	[,3]	[,4]	[,5]	[,6]	[,7]	[,8]	[,9]	[,10]
[1,]	0	0	0	0	0	2	0	2	0	0

And then transform it into a matrix like this (persons x SNIPS)

	[,1]	[,3]	[,4]	[,5]	[,6]	[,8]
[1,]	0	0	1	1	2	2
[2,]	2	1	1	1	2	2
[3,]	0	0	0	0	2	2

I usually use R but if someone do this with pyton i can handle it. If someone can help me it will be really helpfull. Thankyou.

score 1 · Accepted Answer · answered Jul 01 '23 at 19:05

Apply colSums on margin 3.

t(apply(A, 3, colSums))
#      [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
# [1,]    0    0    0    1    1    2    0    2    0     0
# [2,]    2    0    1    1    1    2    0    2    0     0
# [3,]    0    0    0    0    0    2    0    2    0     0

Data:

A <- structure(c(0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 1L, 0L, 1L, 1L, 0L, 
0L, 1L, 1L, 0L, 0L, 0L, 0L, 1L, 1L, 0L, 0L, 0L, 1L, 0L, 1L, 1L, 
0L, 1L, 1L, 0L, 0L, 1L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
0L, 0L, 0L, 0L, 0L, 1L, 1L, 0L, 0L, 1L, 1L, 0L, 0L, 0L, 0L), dim = c(2L, 
10L, 3L))

GWAS array to matrix

1 Answers1