Impact of repetitive DNA on proposed panel All affected regions of length at least 2 are for estimating blood cell counts stopifnot(all(! (panel $ uncovered & panel $ end - panel $ start > 1 ) | panel $ source == " blood-cell-types" For each blood cell type, less than half of regions affected kable(with(panel [panel $ source == " blood-cell-types" uncovered , details )))
affected
total
pct
Blood-NK
3
25
12
Blood-T
6
25
24
Blood-Mono+Macro
9
25
36
Blood-B
10
25
40
Blood-Granul
10
25
40
For each ancestry, less than one-tenth of CpG sites affected kable(with(ancestry ,stats.table(uncovered , ancestry )))
affected
total
pct
ACB
1
50
2
AMR
1
50
2
CDX
1
50
2
CHB
1
50
2
CHS
1
50
2
CLM
1
50
2
EAS
1
50
2
ESN
1
50
2
GWD
1
50
2
ITU
1
50
2
JPT
1
50
2
MSL
1
50
2
SAS
1
50
2
YRI
1
50
2
ASW
2
50
4
FIN
2
50
4
IBS
2
50
4
KHV
2
50
4
LWK
2
50
4
TSI
2
50
4
PUR
3
50
6
PEL
4
50
8
For each episcore, less than 3% of CpG sites affected kable(with(episcores ,stats.table(uncovered ,gene )))
affected
total
pct
IGFBP1
1
120
0.8
TGFA
1
100
1.0
VEGFA
2
159
1.3
HGF
1
72
1.4
OSM
2
125
1.6
CXCL9
1
56
1.8
MMP12
5
257
1.9
S100A12
2
82
2.4
For most remaining sources, less than 2% of CpG sites affected kable(with(panel [! panel $ source %in% c(" blood-cell-types" " ancestry" " episcores" uncovered ,source )))
affected
total
pct
alcohol-consumption
1
314
0.3
bmi
1
397
0.3
crp
1
155
0.6
smoking-cessation
2
222
0.9
hdl
1
89
1.1
dunedin-pace
3
173
1.7
cotinine
2
55
3.6
breast-cancer
4
100
4.0
dunedin-poam38
2
46
4.3