How to use the lsim function

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I would like to check to see if the transfer function I developed through experimentation is correct by using two other transfer functions. This is my code:

%%Loading the data from excel to MATLAB for all trials
P5 = 'P5.csv'; % First trial: gain = 5
P5V2 = 'P5V2.csv'; % Second trial: gain = 5
P5V3 = 'P5V3.csv'; % Third trial: gain = 5
P4 = 'P4.csv'; % Lower gain
P6 = 'P5V3.csv'; % Higher gain
P10 = 'P10.csv';
P15 = 'P15.csv';
P2 = 'P2.csv';
% Reading the xls files into MATLAB
p5 = csvread(P5);
p5v2 = csvread(P5V2);
p5v3 = csvread(P5V3);
p4 = csvread(P4);
p6 = csvread(P6);
p10 = csvread(P10);
p15 = csvread(P15);
p2 = csvread(P2);
%%Analysis Question 1: Version 1 of Gain=5
time = p5(:,1);
output = p5(:,2);
error = p5(:,3);
% Creating a reference signal
% E = S - P, where S is the signal and P is position, then S = E + P
refsig = error + output;
% Plotting motor output vs. time of our best plot with a reference signal on
% the same graph using the hold on function
figure(1)
plot(time, refsig, 'b');
hold on
plot(time, output, 'r');
hold off
title('Motor Position Over a Period of Time at a Gain of 5');
xlabel('Time (s)');
ylabel('Motor Output');
ylim([-80 80]);
legend('Reference Signal','Motor Signal');

So want I would like to do is re-create my reference signal and simulate it in a closed loop using the 'lsim' function in MATLAB. The transfer function I checking is P5 and I am using P6 and P15 to compare the results with. So basically I am just unsure of how to use the lsim function. This is a second order system and I would like to simulate a step input.