data = scan()$data

Not, this is not how R works, try something like

And you need also avoit to mix the headers with the data

my $data = 
"subj1    high    13
subj1    low     15
subj2    high    12
subj2    low     15
subj3    high    16
subj3    low     17
subj4    high    11
subj4    low     18
";

my $R = Statistics::R->new();
$R->startR;
R->send(qq`data <- read.table($data, header = false), sep = "")`);
R->send(qq`names(data) <- c("Subj","Cond","Count")`);
R->send(qq`attach(data)`);
R->send(qq`$Cond <- as.factor($Cond)`);
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