[Bioc-sig-seq] sum of maskedwidth vs. maskedwidth in 'all masks together'

[Joseph Dhahbi, P.h.D.]

Hi

If the masked width is the total number of nucleotide 
positions that are masked, then why the maskedwidth in 
'all masks together:" is not equal to the sum of 
maskedwidth of all 3 masks?
   
> chr2L=Dmelanogaster$chr2L
> chr2L
   23011544-letter "MaskedDNAString" instance (# for 
masking)
seq: 
CGACAATGCACGACAGAGGAAGCAGAACAGATATTTAGATTGCCTCTCATTTTCTCTCCCATATTATAGGGAGAAATAT...CAATCAAACTGTGTTCGAAAAAGAGAAAACTAACATTTTTTTGGCATATTTGCAAATTTTGATGAACCCCCCTTTCAAA
masks:
   maskedwidth  maskedratio active 
                             names
1         200 8.691290e-06  FALSE 
                     assembly gaps
2     1966561 8.545976e-02  FALSE 
                      RepeatMasker
3       61603 2.677048e-03  FALSE Tandem Repeats Finder 
[period<=12]
all masks together:
   maskedwidth maskedratio
       1988181  0.08639929
all active masks together:
   maskedwidth maskedratio
             0           0


> sum(200, 1966561, 61603)
[1] 2028364




Regards,
Joseph

Joseph M. Dhahbi, PhD
Childrens Hospital Oakland Research Institute
5700 Martin Luther King Jr. Way
Oakland, CA 94609
USA
Ph.(510)428-3885 EXT.5743
Cell.(702)335-0795
Fax (510)450-7910
jdhahbi at chori.org
 The email message (and any attachments) is for the sole...{{dropped:3}}