18_preciseTAD_diffWindow_slicing
My Nguyen
2024-04-10
Load data
TAD from Insulation Score
IS - TAD size
## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 65000 185000 265000 374547 400000 24490000
500. PreciseTAD with sliding window of 500 (5KB resolution) and smoothing h = 1100
e = 0.1 and t = 0.1
Arm1
## left_TAD right_TAD center_TAD averageProb_diff error_symetric overlap
## 1 1020000 2060000 1530000 0.3739284 0.03921569 0
## 2 1020000 2410000 1720000 0.5694892 0.01449275 0
## 3 1785000 1925000 1855000 0.4547684 0.00000000 0
## 4 1925000 2060000 1990000 0.2613912 0.07692308 0
## 5 1645000 1785000 1720000 0.2866044 0.15384615 0
## 6 1925000 2060000 1990000 0.2613912 0.07692308 0
## actual_size
## 1 1040000
## 2 1390000
## 3 140000
## 4 135000
## 5 140000
## 6 135000## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 55000 140000 170000 540875 820000 2390000## report error of closest IS boundary and preciseTAD
### Find Distance of closest IS boundaries and preciseTAD boundary
arm.bound.1a = unique(c(report1a$left_TAD, report1a$right_TAD))
closest_IS.bound <- sapply(arm.bound.1a, function(x) {
distances = abs(boundaryIS_ch1$Start - x)
min.d.pos = which(distances == min(distances) )
closest.bound = boundaryIS_ch1$Start[min.d.pos[1]]
return(closest.bound)
} )
report.e_bp <- data.frame(preciseTAD_boundary = arm.bound.1a,
closest_IS.bound)
report.e_bp$error_bp <- abs(report.e_bp$preciseTAD_boundary - report.e_bp$closest_IS.bound)
summary(report.e_bp$error_bp)## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 0 15000 40000 77269 115000 600000plot(density(report.e_bp$error_bp), main = 'Density of Error bp from preciseTAD and closest IS boundary')
print(paste0('Number of overlapped TAD is ', length(which(report.e_bp$error_bp == 0)) ))## [1] "Number of overlapped TAD is 25"
2000. PreciseTAD with sliding window of 2000 (5KB resolution) and smoothing h = 1100
e = 0.1 and t = 0.1
Arm1
## left_TAD right_TAD center_TAD averageProb_diff error_symetric overlap
## 1 900000 2555000 1720000 0.6347220 0.01829268 0
## 2 2410000 2555000 2480000 0.5139072 0.07142857 0
## 3 2555000 3455000 2995000 0.8111084 0.04545455 0
## 4 2555000 3655000 3080000 0.8177772 0.09523810 0
## 5 2555000 3655000 3105000 0.8356176 0.00000000 0
## 6 2555000 3890000 3200000 0.8205000 0.06976744 0
## actual_size
## 1 1655000
## 2 145000
## 3 900000
## 4 1100000
## 5 1100000
## 6 1335000## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 55000 175000 1255000 1584748 2707500 4875000## report error of closest IS boundary and preciseTAD
### Find Distance of closest IS boundaries and preciseTAD boundary
arm.bound.1b = unique(c(report1b$left_TAD, report1b$right_TAD))
closest_IS.bound <- sapply(arm.bound.1b, function(x) {
distances = abs(boundaryIS_ch1$Start - x)
min.d.pos = which(distances == min(distances) )
closest.bound = boundaryIS_ch1$Start[min.d.pos[1]]
return(closest.bound)
} )
report.e_bp <- data.frame(preciseTAD_boundary = arm.bound.1b,
closest_IS.bound)
report.e_bp$error_bp <- abs(report.e_bp$preciseTAD_boundary - report.e_bp$closest_IS.bound)
summary(report.e_bp$error_bp)## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 0 15000 42500 77500 115000 600000plot(density(report.e_bp$error_bp), main = 'Density of Error bp from preciseTAD and closest IS boundary')
print(paste0('Number of overlapped TAD is ', length(which(report.e_bp$error_bp == 0)) ))## [1] "Number of overlapped TAD is 25"
5000. PreciseTAD with sliding window of 5000 (5KB resolution) and smoothing h = 1100
e = 0.1 and t = 0.1
Arm1
## left_TAD right_TAD center_TAD averageProb_diff error_symetric overlap
## 1 900000 2555000 1720000 0.6347220 0.01829268 0
## 2 2410000 2555000 2480000 0.5139072 0.07142857 0
## 3 2555000 3455000 2995000 0.8111084 0.04545455 0
## 4 2555000 3655000 3080000 0.8177772 0.09523810 0
## 5 2555000 3655000 3105000 0.8356176 0.00000000 0
## 6 2555000 3890000 3200000 0.8205000 0.06976744 0
## actual_size
## 1 1655000
## 2 145000
## 3 900000
## 4 1100000
## 5 1100000
## 6 1335000## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 55000 376250 3617500 4547469 7705000 14835000## report error of closest IS boundary and preciseTAD
arm.bound.1c <- unique(c(report1c$left_TAD, report1c$right_TAD))
closest_IS.bound <- sapply(arm.bound.1c, function(x) {
distances = abs(boundaryIS_ch1$Start - x)
min.d.pos = which(distances == min(distances) )
closest.bound = boundaryIS_ch1$Start[min.d.pos[1]]
return(closest.bound)
} )
report.e_bp <- data.frame(preciseTAD_boundary = arm.bound.1c,
closest_IS.bound)
report.e_bp$error_bp <- abs(report.e_bp$preciseTAD_boundary - report.e_bp$closest_IS.bound)
summary(report.e_bp$error_bp)## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 0 15000 45000 79464 120000 600000plot(density(report.e_bp$error_bp), main = 'Density of Error bp from preciseTAD and closest IS boundary')
print(paste0('Number of overlapped TAD is ', length(which(report.e_bp$error_bp == 0)) ))## [1] "Number of overlapped TAD is 26"
7000. PreciseTAD with sliding window of 7000 (5KB resolution) and smoothing h = 1100
e = 0.1 and t = 0.1
Arm1
## left_TAD right_TAD center_TAD averageProb_diff error_symetric overlap
## 1 265000 26840000 12910000 0.8104820 0.10162119 0
## 2 265000 26840000 12955000 0.8065008 0.09416864 0
## 3 265000 26840000 13020000 0.8179160 0.08349667 0
## 4 265000 26840000 13055000 0.8068556 0.07779515 0
## 5 265000 26840000 13135000 0.7944448 0.06487956 0
## 6 265000 26840000 13165000 0.7721396 0.06007752 0
## actual_size
## 1 26575000
## 2 26575000
## 3 26575000
## 4 26575000
## 5 26575000
## 6 26575000## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 55000 356250 8157500 9855754 16195000 34615000## report error of closest IS boundary and preciseTAD
arm.bound.1d <- unique(c(report1d$left_TAD, report1d$right_TAD))
closest_IS.bound <- sapply(arm.bound.1d, function(x) {
distances = abs(boundaryIS_ch1$Start - x)
min.d.pos = which(distances == min(distances) )
closest.bound = boundaryIS_ch1$Start[min.d.pos[1]]
return(closest.bound)
} )
report.e_bp <- data.frame(preciseTAD_boundary = arm.bound.1d,
closest_IS.bound)
report.e_bp$error_bp <- abs(report.e_bp$preciseTAD_boundary - report.e_bp$closest_IS.bound)
summary(report.e_bp$error_bp)## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 0 15000 45000 80099 121250 600000plot(density(report.e_bp$error_bp), main = 'Density of Error bp from preciseTAD and closest IS boundary')
print(paste0('Number of overlapped TAD is ', length(which(report.e_bp$error_bp == 0)) ))## [1] "Number of overlapped TAD is 25"