Comments (2)
PG0389-C,
dd2 will definitely be wrong at
Ref 3d7/dd2 is 0/1, but there is alt read in the data
length(which(panel$dd2gt.from.regression == 1 & coverage$altCount==0))/length(panel$dd2gt.from.regression)
[1] 0.09504577
dd2 or 3d7 will be wrong at Ref is 0/0,
length(which(panel$dd2gt.from.regression == 0 & coverage$altCount>0))/length(panel$dd2gt.from.regression)
[1] 0.01357027
from deploidpaper.
PG0402-C,
hb3/7g8, will definitely be wrong at 0/0
length(which(panel$HB3gt.from.regression == 0 & panel$sevenG8gt.from.regression == 0 & coverage$altCount>0))/length(panel$dd2gt.from.regression)
[1] 0.01631664
hb3/7g8, will definitely be wrong at 1/1
length(which(panel$HB3gt.from.regression == 1 & panel$sevenG8gt.from.regression == 1 & coverage$altCount==0))/length(panel$dd2gt.from.regression)
[1] 0.0001077006
Hb3 is definitely wrong at
length(which(panel$HB3gt.from.regression == 1 & panel$sevenG8gt.from.regression == 0 & coverage$altCount==0))/length(panel$dd2gt.from.regression)
[1] 0.0008616047
7g8 is definitely wrong at
length(which(panel$HB3gt.from.regression == 0 & panel$sevenG8gt.from.regression == 1 & coverage$altCount==0))/length(panel$dd2gt.from.regression)
[1] 0.02261712
7g8 is minor strain, hb3/7g8 as 0/1, and the data strongly suggest alt
length(which(panel$HB3gt.from.regression == 0 & panel$sevenG8gt.from.regression == 1 & coverage$altCount>30))/length(panel$dd2gt.from.regression)
from deploidpaper.
Related Issues (17)
- post = likelihood \times prior
- benchmark scripts HOT 1
- reviewer 1 comment HOT 7
- Reviewer 2 comment HOT 2
- reviewer 3 comments HOT 3
- need to rerun painting for supplement
- need to do multiple runs, and get a range for the proportions
- deconvolute elife asia/africa mixed samples
- simulation study for computing the errors HOT 1
- all example use PG0412
- rm tmp files and replot HOT 1
- 3D7 Dd2 HB3 7G8
- wsaf of sim1 vs sim2
- paper structure
- nature methods todo list HOT 1
- vs coil HOT 1
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from deploidpaper.