Instead of inputting the entire array into findpeaks, you can simply input the part of the array you want to search, and then adjust the outputted indices appropriately.
% a signal with some peaks
t = 0:0.01:8*pi;
y = sin(t);
plot(t,y)
ylim([-1.1 1.1]);
hold on
% find the locations of the peaks in y
[~,idx] = findpeaks(y)
% plot them in red
plot(t(idx),y(idx),'ro','MarkerFaceColor','r')
% now find the peaks just among index 500 to index 1500 of y
[~,idx] = findpeaks(y(500:1500))
% adjust the indices of the peaks
% (index 1 in y(500:1500) corresponds to index 500 in y)
idx = idx+499
% plot them in green
plot(t(idx),y(idx),'g.')
% show the search region for reference
xline(t([500 1500]),'--')
