BIOS is Basic I/O System, it uses the Power On Self Test (POST) software to check the hardware before Windows is loaded. BIOS also saves settings like date and time. If more than 1 short beep is given it means that something hardware level is wrong, 1 beep (or nothing) means that everything is alright according to the check.
In the advanced troubleshooting options, open command prompt and enter
chkdsk C: /r
sfc /scannow
C: is assumed that the Windows partition letter is C, if it isn't change C to the letter of the Windows partition.
To check what the Windows partition letter is, run following commands, the one with 'Boot' under info is the Windows partition.
diskpart
list volume
NOTE: it may take several hours for the commands to finish. DO NOT interrupt it in any way, interruption could cause the system to become unbootable and repair may be more difficult.