connect two matrixes by columns and extract sub matrix - r

Question

I have two matrixes (e.g., A and B). I would like to extract columns of B based on the order of A's first column:
For example
matrix A
name score
a 0.1
b 0.2
c 0.1
d 0.6
matrix B
a d b c g h
0.1 0.2 0.3 0.4 0.6 0.2
0.2 0.1 0.4 0.7 0.1 0.1
...
I want matrix B to look like this at the end
matrix B_modified
a b c d
0.1 0.3 0.4 0.2
0.2 0.4 0.7 0.1
Can this be done either in perl or R? thanks a lot in advance

Answer 1

I've no idea what problems you're facing. Here's how I've done it.
## get data as matrix
a <- read.table(header=TRUE, text="name score
a 0.1
b 0.2
c 0.1
d 0.6", stringsAsFactors=FALSE) # load directly as characters
b <- read.table(header=TRUE, text="a d b c g h
0.1 0.2 0.3 0.4 0.6 0.2
0.2 0.1 0.4 0.7 0.1 0.1", stringsAsFactors=FALSE)
a <- as.matrix(a)
b <- as.matrix(b)
Now subset to get your final result:
b[, a[, "name"]]
# a b c d
# [1,] 0.1 0.3 0.4 0.2
# [2,] 0.2 0.4 0.7 0.1

Answer 2

The error :
[.data.frame(b, , a[, "name"]) : undefined columns selected
means that you try to get a column non defined in b but exist in a$name. One solution is to use intersect with colnames(b). This will convert also the factor to a string and you get the right order.
b[, intersect(a[, "name"],colnames(b))] ## the order is important here
For example , I test this with this data:
b <- read.table(text='
a d b c
0.1 0.2 0.3 0.4
0.2 0.1 0.4 0.7',header=TRUE)
a <- read.table(text='name score
a 0.1
z 0.5
c 0.1
d 0.6',header=TRUE)
b[, intersect(a[, "name"],colnames(b))]
a c d
1 0.1 0.4 0.2
2 0.2 0.7 0.1

Answer 3

If your data originates as an R data structure then it would be perverse to export it and solve this problem using Perl. However, if you have text files that look like the data you have shown, then here is a Perl solution for you.
I have split the output on spaces. That can be changed very simply if necessary.
use strict;
use warnings;
use autodie;
sub read_file {
my ($name) = #_;
open my $fh, '<', $name;
my #data = map [ split ], <$fh>;
\#data;
}
my $matrix_a = read_file('MatrixA.txt');
my #fields = map $matrix_a->[$_][0], 1 .. $#$matrix_a;
my $matrix_b = read_file('MatrixB.txt');
my #headers = #{$matrix_b->[0]};
my #indices = map {
my $label = $_;
grep $headers[$_] eq $label, 0..$#headers
} #fields;
for my $row (0 .. $#$matrix_b) {
print join(' ', map $matrix_b->[$row][$_], #indices), "\n";
}
output
a b c d
0.1 0.3 0.4 0.2
0.2 0.4 0.7 0.1