combination_index: compute combination index
In MACSQuantifyR: Fast treatment of MACSQuantify FACS data
Description
Usage
Arguments
Value
References
Examples
View source: R/combination_index.R
Description
This function allows the user to compute combination index
on the drug combinations. This function also generates intermediary
plots and tables.
Usage
1
Arguments
MACSQuant
object of class MACSQuant resulting of the function
load_maxQuant().
Contains the original data table
...
params for lattice cloud namely z and x for parameter screen
default for z and x are c(-110,-70) and argument xlab and ylab
Value
Several plots and combination index
References
Chou, T. C. (2006). Theoretical basis, experimental design, and
computerized simulation of synergism and antagonism in drug
combination studies. Pharmacological reviews, 58(3), 621-681.
Examples
1
2
3
4
filepath <- system.file("extdata", "drugs.Rdata",
package = "MACSQuantifyR")
load(filepath)
combination_index(MACSQuant)
Example output
`geom_smooth()` using formula 'y ~ x'
An object of class "MACSQuant"
Slot "my_data":
# A tibble: 128 x 4
`Full path` WID `%-#` `Count/mL`
<chr> <chr> <dbl> <dbl>
1 "99ko plate 1 unst.0001\\P1" A2 89.2 878032.
2 "99ko plate 1 unst.0001\\P1\\P2\\DAPI" A2 1.15 8893.
3 "99ko plate 1.0004\\P1" E1 91.0 510978.
4 "99ko plate 1.0004\\P1\\P2\\DAPI" E1 34.2 144757.
5 "99ko plate 1.0005\\P1" F1 89.6 464565.
6 "99ko plate 1.0005\\P1\\P2\\DAPI" F1 34.4 127844.
7 "99ko plate 1.0006\\P1" G1 74.4 87400
8 "99ko plate 1.0006\\P1\\P2\\DAPI" G1 37.4 25400
9 "99ko plate 1.0007\\P1" B2 85.6 482630.
10 "99ko plate 1.0007\\P1\\P2\\DAPI" B2 23.6 94017.
# … with 118 more rows
Slot "my_data_sorted":
# A tibble: 120 x 4
`Full path` WID `%-#` `Count/mL`
<chr> <chr> <dbl> <dbl>
1 "99ko plate 1.0013\\P1" B3 87.3 657284.
2 "99ko plate 1.0013\\P1\\P2\\DAPI" B3 24.9 130464.
3 "99ko plate 1.0014\\P1" C3 85.6 510888.
4 "99ko plate 1.0014\\P1\\P2\\DAPI" C3 24.3 99698.
5 "99ko plate 1.0015\\P1" D3 84.7 505841.
6 "99ko plate 1.0015\\P1\\P2\\DAPI" D3 24.7 99221.
7 "99ko plate 1.0021\\P1" D4 88.9 616191.
8 "99ko plate 1.0021\\P1\\P2\\DAPI" D4 26.7 128201.
9 "99ko plate 1.0020\\P1" C4 89.1 630008.
10 "99ko plate 1.0020\\P1\\P2\\DAPI" C4 25.0 123357.
# … with 110 more rows
Slot "my_replicates_sorted":
[,1] [,2] [,3]
[1,] "B3" "C3" "D3"
[2,] "D4" "C4" "B4"
[3,] "B5" "C5" "D5"
[4,] "D6" "C6" "B6"
[5,] "B7" "C7" "D7"
[6,] "D8" "C8" "B8"
[7,] "B9" "C9" "D9"
[8,] "E1" "F1" "G1"
[9,] "G2" "F2" "E2"
[10,] "E3" "F3" "G3"
[11,] "G4" "F4" "E4"
[12,] "E5" "F5" "G5"
[13,] "G6" "F6" "E6"
[14,] "E7" "F7" "G7"
[15,] "G8" "F8" "E8"
[16,] "E9" "F9" "G9"
[17,] "G10" "F10" "E10"
[18,] "E11" "F11" "G11"
[19,] "G12" "F12" "E12"
[20,] "D10" "C10" "B10"
Slot "experiment_name":
[1] "Combo drug1-drug2 HC line 101"
Slot "statistics":
Full.path.first WID.first Fluo.percent.plus Fluo.percent.minus
1 99ko plate 1.0013 B3 0.2462000 0.753800000
2 99ko plate 1.0021 D4 0.2551333 0.744866667
3 99ko plate 1.0025 B5 0.3314667 0.668533333
4 99ko plate 1.0033 D6 0.7760333 0.223966667
5 99ko plate 1.0037 B7 0.3551667 0.644833333
6 99ko plate 1.0045 D8 0.3786000 0.621400000
7 99ko plate 1.0049 B9 0.3815000 0.618500000
8 99ko plate 1.0004 E1 0.3534333 0.646566667
9 99ko plate 1.0012 G2 0.6734333 0.326566667
10 99ko plate 1.0016 E3 0.8816333 0.118366667
11 99ko plate 1.0024 G4 0.9814333 0.018566667
12 99ko plate 1.0028 E5 0.3957333 0.604266667
13 99ko plate 1.0036 G6 0.7300333 0.269966667
14 99ko plate 1.0040 E7 0.9215667 0.078433333
15 99ko plate 1.0048 G8 0.9903667 0.009633333
16 99ko plate 1.0052 E9 0.4776667 0.522333333
17 99ko plate 1.0060 G10 0.7890333 0.210966667
18 99ko plate 1.0064 E11 0.9503000 0.049700000
19 99ko plate 1.0069 G12 0.9913333 0.008666667
20 99ko plate 1.0063 D10 0.9993000 0.000700000
sd_percent Cell.count.minus sd_count
1 0.0026229754 448209.740 68116.3192
2 0.0101962411 497333.267 9330.2382
3 0.0062171805 501780.027 18721.3278
4 0.0043247351 129869.363 5227.2472
5 0.0281894188 326411.763 35176.7929
6 0.0200920382 308638.050 24277.3684
7 0.0151565168 304014.930 16363.7384
8 0.0181731487 254980.660 167775.7546
9 0.0522871240 139098.410 96569.6019
10 0.0150387278 58429.607 32069.2551
11 0.0075639496 12433.970 8660.4721
12 0.0460228566 201109.040 167105.5841
13 0.0650526966 128413.763 108761.1608
14 0.0264942132 3934.470 2358.0845
15 0.0060335175 5386.383 8471.7742
16 0.0766065489 98992.863 149545.3756
17 0.0795396966 59399.013 94953.8684
18 0.0340048526 21850.097 35648.1022
19 0.0043131582 4183.147 6763.1225
20 0.0005567764 2627.213 173.1322
Slot "combination.index.df":
doses1_c doses2_c fa_c CI doses1_c_norm doses2_c_norm
1 1 10 0.3534333 0.35126455 0.35124491 1.964114e-05
2 3 10 0.6734333 0.25224413 0.25223943 4.701630e-06
3 5 10 0.8816333 0.10546105 0.10545987 1.179435e-06
4 10 10 0.9814333 0.02556716 0.02556701 1.429673e-07
5 1 50 0.3957333 0.28921697 0.28913612 8.084052e-05
6 3 50 0.7300333 0.18840941 0.18839185 1.755770e-05
7 5 50 0.9215667 0.06455628 0.06455267 3.609699e-06
8 10 50 0.9903667 0.01249138 0.01249103 3.492407e-07
9 1 100 0.4776667 0.20193171 0.20181885 1.128544e-04
10 3 100 0.7890333 0.13288494 0.13286017 2.476454e-05
11 5 100 0.9503000 0.03821565 0.03821138 4.273458e-06
12 10 100 0.9913333 0.01113562 0.01113500 6.226540e-07
DX1 DX2 Decision Color Condition
1 0.35124491 1.964114e-05 Synergism orange 8
2 0.25223943 4.701630e-06 Strong Synergism red 9
3 0.10545987 1.179435e-06 Strong Synergism red 10
4 0.02556701 1.429673e-07 Very Strong Synergism darkred 11
5 0.28913612 8.084052e-05 Strong Synergism red 12
6 0.18839185 1.755770e-05 Strong Synergism red 13
7 0.06455267 3.609699e-06 Very Strong Synergism darkred 14
8 0.01249103 3.492407e-07 Very Strong Synergism darkred 15
9 0.20181885 1.128544e-04 Strong Synergism red 16
10 0.13286017 2.476454e-05 Strong Synergism red 17
11 0.03821138 4.273458e-06 Very Strong Synergism darkred 18
12 0.01113500 6.226540e-07 Very Strong Synergism darkred 19
Slot "param.experiment":
$number_of_replicates
[1] 3
$number_of_conditions
[1] 19
$doses
[1] 1 3 5 10 0 0 0 1 3 5 10 1 3 5 10 1 3 5 10
$doses.alt
[1] 0 0 0 0 10 50 100 10 10 10 10 50 50 50 50 100 100 100 100
$c_names
[1] "Drug1_c1" "Drug1_c2" "Drug1_c3" "Drug1_c4" "Drug2_c1"
[6] "Drug2_c2" "Drug2_c3" "D2[1]_D1[1]" "D2[1]_D1[2]" "D2[1]_D1[3]"
[11] "D2[1]_D1[4]" "D2[2]_D1[1]" "D2[2]_D1[2]" "D2[2]_D1[3]" "D2[2]_D1[4]"
[16] "D2[3]_D1[1]" "D2[3]_D1[2]" "D2[3]_D1[3]" "D2[3]_D1[4]"
$control
[1] TRUE
Slot "param.output":
$plt.title
character(0)
$plt.labels
[1] "Drug1_c1" "Drug1_c2" "Drug1_c3" "Drug1_c4" "Drug2_c1"
[6] "Drug2_c2" "Drug2_c3" "D2[1]_D1[1]" "D2[1]_D1[2]" "D2[1]_D1[3]"
[11] "D2[1]_D1[4]" "D2[2]_D1[1]" "D2[2]_D1[2]" "D2[2]_D1[3]" "D2[2]_D1[4]"
[16] "D2[3]_D1[1]" "D2[3]_D1[2]" "D2[3]_D1[3]" "D2[3]_D1[4]" "Control"
$save.files
[1] FALSE
$path
[1] "."
$plt.col
[1] "#FF0000FF" "#FF1200FF" "#FF2400FF" "#FF3700FF" "#FF4900FF" "#FF5B00FF"
[7] "#FF6D00FF" "#FF8000FF" "#FF9200FF" "#FFA400FF" "#FFB600FF" "#FFC800FF"
[13] "#FFDB00FF" "#FFED00FF" "#FFFF00FF" "#FFFF20FF" "#FFFF60FF" "#FFFF9FFF"
[19] "#FFFFDFFF" "1"
Warning messages:
1: Use of `dose_rep_df$dataset` is discouraged. Use `dataset` instead.
2: Use of `dose_rep_df$dataset` is discouraged. Use `dataset` instead.
3: Use of `dose_rep_df$dataset` is discouraged. Use `dataset` instead.
4: Use of `CI_df$Decision` is discouraged. Use `Decision` instead.
MACSQuantifyR documentation built on Nov. 8, 2020, 5:08 p.m.
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Description Usage Arguments Value References Examples
View source: R/combination_index.R
Description
This function allows the user to compute combination index on the drug combinations. This function also generates intermediary plots and tables.
Usage
1 |
Arguments
MACSQuant |
object of class MACSQuant resulting of the function load_maxQuant(). Contains the original data table |
... |
params for lattice cloud namely z and x for parameter screen default for z and x are c(-110,-70) and argument xlab and ylab |
Value
Several plots and combination index
References
Chou, T. C. (2006). Theoretical basis, experimental design, and computerized simulation of synergism and antagonism in drug combination studies. Pharmacological reviews, 58(3), 621-681.
Examples
1 2 3 4 | filepath <- system.file("extdata", "drugs.Rdata",
package = "MACSQuantifyR")
load(filepath)
combination_index(MACSQuant)
|
Example output
`geom_smooth()` using formula 'y ~ x'
An object of class "MACSQuant"
Slot "my_data":
# A tibble: 128 x 4
`Full path` WID `%-#` `Count/mL`
<chr> <chr> <dbl> <dbl>
1 "99ko plate 1 unst.0001\\P1" A2 89.2 878032.
2 "99ko plate 1 unst.0001\\P1\\P2\\DAPI" A2 1.15 8893.
3 "99ko plate 1.0004\\P1" E1 91.0 510978.
4 "99ko plate 1.0004\\P1\\P2\\DAPI" E1 34.2 144757.
5 "99ko plate 1.0005\\P1" F1 89.6 464565.
6 "99ko plate 1.0005\\P1\\P2\\DAPI" F1 34.4 127844.
7 "99ko plate 1.0006\\P1" G1 74.4 87400
8 "99ko plate 1.0006\\P1\\P2\\DAPI" G1 37.4 25400
9 "99ko plate 1.0007\\P1" B2 85.6 482630.
10 "99ko plate 1.0007\\P1\\P2\\DAPI" B2 23.6 94017.
# … with 118 more rows
Slot "my_data_sorted":
# A tibble: 120 x 4
`Full path` WID `%-#` `Count/mL`
<chr> <chr> <dbl> <dbl>
1 "99ko plate 1.0013\\P1" B3 87.3 657284.
2 "99ko plate 1.0013\\P1\\P2\\DAPI" B3 24.9 130464.
3 "99ko plate 1.0014\\P1" C3 85.6 510888.
4 "99ko plate 1.0014\\P1\\P2\\DAPI" C3 24.3 99698.
5 "99ko plate 1.0015\\P1" D3 84.7 505841.
6 "99ko plate 1.0015\\P1\\P2\\DAPI" D3 24.7 99221.
7 "99ko plate 1.0021\\P1" D4 88.9 616191.
8 "99ko plate 1.0021\\P1\\P2\\DAPI" D4 26.7 128201.
9 "99ko plate 1.0020\\P1" C4 89.1 630008.
10 "99ko plate 1.0020\\P1\\P2\\DAPI" C4 25.0 123357.
# … with 110 more rows
Slot "my_replicates_sorted":
[,1] [,2] [,3]
[1,] "B3" "C3" "D3"
[2,] "D4" "C4" "B4"
[3,] "B5" "C5" "D5"
[4,] "D6" "C6" "B6"
[5,] "B7" "C7" "D7"
[6,] "D8" "C8" "B8"
[7,] "B9" "C9" "D9"
[8,] "E1" "F1" "G1"
[9,] "G2" "F2" "E2"
[10,] "E3" "F3" "G3"
[11,] "G4" "F4" "E4"
[12,] "E5" "F5" "G5"
[13,] "G6" "F6" "E6"
[14,] "E7" "F7" "G7"
[15,] "G8" "F8" "E8"
[16,] "E9" "F9" "G9"
[17,] "G10" "F10" "E10"
[18,] "E11" "F11" "G11"
[19,] "G12" "F12" "E12"
[20,] "D10" "C10" "B10"
Slot "experiment_name":
[1] "Combo drug1-drug2 HC line 101"
Slot "statistics":
Full.path.first WID.first Fluo.percent.plus Fluo.percent.minus
1 99ko plate 1.0013 B3 0.2462000 0.753800000
2 99ko plate 1.0021 D4 0.2551333 0.744866667
3 99ko plate 1.0025 B5 0.3314667 0.668533333
4 99ko plate 1.0033 D6 0.7760333 0.223966667
5 99ko plate 1.0037 B7 0.3551667 0.644833333
6 99ko plate 1.0045 D8 0.3786000 0.621400000
7 99ko plate 1.0049 B9 0.3815000 0.618500000
8 99ko plate 1.0004 E1 0.3534333 0.646566667
9 99ko plate 1.0012 G2 0.6734333 0.326566667
10 99ko plate 1.0016 E3 0.8816333 0.118366667
11 99ko plate 1.0024 G4 0.9814333 0.018566667
12 99ko plate 1.0028 E5 0.3957333 0.604266667
13 99ko plate 1.0036 G6 0.7300333 0.269966667
14 99ko plate 1.0040 E7 0.9215667 0.078433333
15 99ko plate 1.0048 G8 0.9903667 0.009633333
16 99ko plate 1.0052 E9 0.4776667 0.522333333
17 99ko plate 1.0060 G10 0.7890333 0.210966667
18 99ko plate 1.0064 E11 0.9503000 0.049700000
19 99ko plate 1.0069 G12 0.9913333 0.008666667
20 99ko plate 1.0063 D10 0.9993000 0.000700000
sd_percent Cell.count.minus sd_count
1 0.0026229754 448209.740 68116.3192
2 0.0101962411 497333.267 9330.2382
3 0.0062171805 501780.027 18721.3278
4 0.0043247351 129869.363 5227.2472
5 0.0281894188 326411.763 35176.7929
6 0.0200920382 308638.050 24277.3684
7 0.0151565168 304014.930 16363.7384
8 0.0181731487 254980.660 167775.7546
9 0.0522871240 139098.410 96569.6019
10 0.0150387278 58429.607 32069.2551
11 0.0075639496 12433.970 8660.4721
12 0.0460228566 201109.040 167105.5841
13 0.0650526966 128413.763 108761.1608
14 0.0264942132 3934.470 2358.0845
15 0.0060335175 5386.383 8471.7742
16 0.0766065489 98992.863 149545.3756
17 0.0795396966 59399.013 94953.8684
18 0.0340048526 21850.097 35648.1022
19 0.0043131582 4183.147 6763.1225
20 0.0005567764 2627.213 173.1322
Slot "combination.index.df":
doses1_c doses2_c fa_c CI doses1_c_norm doses2_c_norm
1 1 10 0.3534333 0.35126455 0.35124491 1.964114e-05
2 3 10 0.6734333 0.25224413 0.25223943 4.701630e-06
3 5 10 0.8816333 0.10546105 0.10545987 1.179435e-06
4 10 10 0.9814333 0.02556716 0.02556701 1.429673e-07
5 1 50 0.3957333 0.28921697 0.28913612 8.084052e-05
6 3 50 0.7300333 0.18840941 0.18839185 1.755770e-05
7 5 50 0.9215667 0.06455628 0.06455267 3.609699e-06
8 10 50 0.9903667 0.01249138 0.01249103 3.492407e-07
9 1 100 0.4776667 0.20193171 0.20181885 1.128544e-04
10 3 100 0.7890333 0.13288494 0.13286017 2.476454e-05
11 5 100 0.9503000 0.03821565 0.03821138 4.273458e-06
12 10 100 0.9913333 0.01113562 0.01113500 6.226540e-07
DX1 DX2 Decision Color Condition
1 0.35124491 1.964114e-05 Synergism orange 8
2 0.25223943 4.701630e-06 Strong Synergism red 9
3 0.10545987 1.179435e-06 Strong Synergism red 10
4 0.02556701 1.429673e-07 Very Strong Synergism darkred 11
5 0.28913612 8.084052e-05 Strong Synergism red 12
6 0.18839185 1.755770e-05 Strong Synergism red 13
7 0.06455267 3.609699e-06 Very Strong Synergism darkred 14
8 0.01249103 3.492407e-07 Very Strong Synergism darkred 15
9 0.20181885 1.128544e-04 Strong Synergism red 16
10 0.13286017 2.476454e-05 Strong Synergism red 17
11 0.03821138 4.273458e-06 Very Strong Synergism darkred 18
12 0.01113500 6.226540e-07 Very Strong Synergism darkred 19
Slot "param.experiment":
$number_of_replicates
[1] 3
$number_of_conditions
[1] 19
$doses
[1] 1 3 5 10 0 0 0 1 3 5 10 1 3 5 10 1 3 5 10
$doses.alt
[1] 0 0 0 0 10 50 100 10 10 10 10 50 50 50 50 100 100 100 100
$c_names
[1] "Drug1_c1" "Drug1_c2" "Drug1_c3" "Drug1_c4" "Drug2_c1"
[6] "Drug2_c2" "Drug2_c3" "D2[1]_D1[1]" "D2[1]_D1[2]" "D2[1]_D1[3]"
[11] "D2[1]_D1[4]" "D2[2]_D1[1]" "D2[2]_D1[2]" "D2[2]_D1[3]" "D2[2]_D1[4]"
[16] "D2[3]_D1[1]" "D2[3]_D1[2]" "D2[3]_D1[3]" "D2[3]_D1[4]"
$control
[1] TRUE
Slot "param.output":
$plt.title
character(0)
$plt.labels
[1] "Drug1_c1" "Drug1_c2" "Drug1_c3" "Drug1_c4" "Drug2_c1"
[6] "Drug2_c2" "Drug2_c3" "D2[1]_D1[1]" "D2[1]_D1[2]" "D2[1]_D1[3]"
[11] "D2[1]_D1[4]" "D2[2]_D1[1]" "D2[2]_D1[2]" "D2[2]_D1[3]" "D2[2]_D1[4]"
[16] "D2[3]_D1[1]" "D2[3]_D1[2]" "D2[3]_D1[3]" "D2[3]_D1[4]" "Control"
$save.files
[1] FALSE
$path
[1] "."
$plt.col
[1] "#FF0000FF" "#FF1200FF" "#FF2400FF" "#FF3700FF" "#FF4900FF" "#FF5B00FF"
[7] "#FF6D00FF" "#FF8000FF" "#FF9200FF" "#FFA400FF" "#FFB600FF" "#FFC800FF"
[13] "#FFDB00FF" "#FFED00FF" "#FFFF00FF" "#FFFF20FF" "#FFFF60FF" "#FFFF9FFF"
[19] "#FFFFDFFF" "1"
Warning messages:
1: Use of `dose_rep_df$dataset` is discouraged. Use `dataset` instead.
2: Use of `dose_rep_df$dataset` is discouraged. Use `dataset` instead.
3: Use of `dose_rep_df$dataset` is discouraged. Use `dataset` instead.
4: Use of `CI_df$Decision` is discouraged. Use `Decision` instead.
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