readMacSynergyValues: Read data from macsynergyII formate and clean for outliers
In COMBIA: Synergy/Antagonism Analyses of Drug Combinations
Description
Usage
Arguments
Value
Author(s)
Examples
Description
Read data from macsynergyII formate and clean for outliers
Usage
1
2
readMacSynergyValues(file, sheet, nrow = 41, wellRangesExcel,
minThersholdForCVCal, minThersholdForCV, survivalFunc)
Arguments
file
Name of fiele to be read
sheet
Sheet Number
nrow
Number of rows in the sheet
wellRangesExcel
TRUE if wells in excel formate
minThersholdForCVCal
Thresolld for data outliears in CV
minThersholdForCV
Thresold of values in CV not to remove
survivalFunc
<- function (x,y,z) (x-z)/(y-z) # It can be any function
Value
Matrix of replicated values
Author(s)
Muhammad kashif
Examples
1
2
3
4
5
6
7
8
9
fl <- system.file("extdata", "testData.csv", package="COMBIA")
sh <- 1
wellR <- list(c( "l3:l10","m3:m10","b3:k10", "l13:l20","m13:m20","b13:k20",
"l23:l30","m23:m30","b23:k30", "l33:l40","m33:m40","b33:k40"))
minThersholdForCV <- 0.3
minThersholdForCVCal <- 0.1
survivalFunc <- function (x,y,z) {(x-z)/(y-z)}
rslt <- readMacSynergyValues(fl, sh, nrow=41, wellR,
minThersholdForCVCal, minThersholdForCV, survivalFunc)
Example output
Loading required package: hash
hash-3.0.1 provided by Decision Patterns
Loading required package: lattice
Loading required package: latticeExtra
Loading required package: RColorBrewer
Loading required package: oro.nifti
oro.nifti 0.9.1
[1] "Ratio between empty and control 215.34756097561"
[1] "CV for control: 1 : 2.30698484671909"
[1] "Ratio between empty and control 216.431571815718"
[1] "CV for control: 2 : 3.97477131010254"
[1] "Ratio between empty and control 212.255570117955"
[1] "CV for control: 3 : 6.4008999376604"
[1] "Ratio between empty and control 191.453473132372"
[1] "CV for control: 4 : 5.87005801002331"
[1] "Number of the variable datapoints before data removal= 22"
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,] 0.4959273 0.4544325 0.4527889 0.5141335 0.7657826 0.8754745 0.9742680
[2,] 0.5282520 0.4508880 0.4907902 0.5426933 0.7353865 0.9182928 0.9180664
[3,] 0.4939636 0.4681056 0.5032695 0.5585093 0.7629166 0.8590776 0.9670757
[4,] 0.5893432 0.5392455 0.5748920 0.6414779 0.8667800 0.9914462 1.0411311
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] 0.9653167 0.3883595 0.4311439 0.5377761 0.5499641 0.7446938 0.8205780
[2,] 0.8856867 0.4417552 0.5078481 0.5198489 0.6046601 0.7495008 0.8080710
[3,] 1.0026615 0.3025846 0.4016490 0.5368700 0.5787590 0.7088183 0.8592761
[4,] 0.9958504 0.4488219 0.5907471 0.5606334 0.6452214 0.7078161 0.8624584
[,15] [,16] [,17] [,18] [,19] [,20] [,21]
[1,] 0.9662776 0.9516621 0.3719992 0.4589335 0.5391416 0.5714069 0.6952844
[2,] 0.8874478 0.8987191 0.4345346 0.5168550 0.5483290 0.5782179 0.6729921
[3,] 0.9738752 0.9966561 0.3164069 0.4027905 0.5139402 0.5712646 0.7147492
[4,] 0.9743249 0.8783960 0.4989471 0.5837279 0.5916279 0.6235858 0.7095227
[,22] [,23] [,24] [,25] [,26] [,27] [,28]
[1,] 0.8367865 0.9272861 0.9249851 0.00000000 0.2005835 0.3076203 0.5062694
[2,] 0.8237954 0.8538857 0.8311670 0.08167886 0.2314255 0.0000000 0.3672844
[3,] 0.8314577 0.9330037 0.9559334 0.06050699 0.0000000 0.1937179 0.4452006
[4,] 0.8354551 0.8611646 0.8680737 0.05142586 0.0000000 0.1851207 0.6040147
[,29] [,30] [,31] [,32] [,33] [,34] [,35]
[1,] 0.4562531 0.6521713 0.6713130 0.7385240 0.05020593 0.05465631 0.06740060
[2,] 0.4803995 0.5218113 0.6356309 0.6285863 0.03475723 0.05490963 0.06658343
[3,] 0.4499404 0.6100268 0.6939040 0.8689294 0.02834578 0.04132442 0.06430379
[4,] 0.4855143 0.5217113 0.6216590 0.6994481 0.03135924 0.05079276 0.00000000
[,36] [,37] [,38] [,39] [,40] [,41] [,42]
[1,] 0.12429475 0.1606059 0.2181069 0.2718402 0.3368766 0.02754941 0.04739915
[2,] 0.08167886 0.1406768 0.2105184 0.2518295 0.3291433 0.03548684 0.04884630
[3,] 0.08065737 0.1508611 0.1835683 0.2876951 0.3136276 0.03569124 0.04281336
[4,] 0.13160973 0.2082152 0.2306766 0.3238528 0.3092915 0.05068265 0.04264499
[,43] [,44] [,45] [,46] [,47] [,48] [,49]
[1,] 0.06808333 0.08942496 0.1572175 0.1623506 0.2106727 0.2543674 0.01933137
[2,] 0.07347701 0.11561843 0.1250531 0.1410291 0.2056878 0.2528611 0.03053051
[3,] 0.08353600 0.08701020 0.1579832 0.2060017 0.3179703 0.2390066 0.02948731
[4,] 0.11102012 0.08302596 0.1467216 0.1699538 0.2212626 0.2220058 0.04085579
[,50] [,51] [,52] [,53] [,54] [,55] [,56]
[1,] 0.03738578 0.06740060 0.09645455 0.1303635 0.1664470 0.1984847 0.2228354
[2,] 0.04690905 0.06693566 0.07219390 0.1162222 0.1463879 0.1632948 0.1580617
[3,] 0.05544457 0.08321339 0.11244634 0.1846601 0.1907400 0.2458806 0.2747413
[4,] 0.05445374 0.08222770 0.12626965 0.1550896 0.2057103 0.2272083 0.2090685
[,57] [,58] [,59] [,60] [,61] [,62] [,63]
[1,] 0.01025359 0.01930608 0.04671642 0.04841060 0.10983099 0.1492017 0.1828325
[2,] 0.03060599 0.03719766 0.05735006 0.04758835 0.10417106 0.1408530 0.1359973
[3,] 0.01926322 0.05350895 0.05651165 0.08440455 0.09614239 0.1644601 0.1522012
[4,] 0.02222054 0.04581051 0.04608577 0.06967574 0.11129538 0.1729541 0.1654670
[,64] [,65] [,66] [,67] [,68] [,69]
[1,] 0.0000000 -0.0005689415 0.001226385 0.006915800 0.001555107 0.007674388
[2,] 0.1718489 0.0030316658 0.001496964 0.002729757 0.015233806 0.041273425
[3,] 0.1958769 0.0100813956 0.008840608 0.015441596 0.042292230 0.029065439
[4,] 0.1998748 0.0032825016 0.011320157 0.007466487 0.002208979 0.045507721
[,70] [,71] [,72] [,73] [,74] [,75]
[1,] 0.005423909 0.03877652 0.00643536 0.000265506 0.0006700866 0.0003160786
[2,] 0.012994651 0.04655683 0.02595156 0.001673077 0.0009434645 0.0061765474
[3,] 0.012165918 0.04110107 0.02296077 0.002115542 0.0017184902 0.0017184902
[4,] 0.019302761 0.02464285 0.09648628 0.001135457 0.0005849321 0.0001720389
[,76] [,77] [,78] [,79] [,80]
[1,] -2.149334e-04 0.0003919375 -0.0002402197 0.0016056793 0.0011758124
[2,] 5.157606e-04 0.0005157606 0.0001383748 0.0020756218 0.0010189416
[3,] -1.861181e-05 0.0013958855 0.0001799141 0.0007258605 0.0001302827
[4,] 1.720389e-04 0.0014657711 0.0008601943 0.0012730876 -0.0002959069
[1] "Number of the variable datapoints after data removal= 17"
COMBIA documentation built on May 2, 2019, 7:23 a.m.
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Description Usage Arguments Value Author(s) Examples
Description
Read data from macsynergyII formate and clean for outliers
Usage
1 2 | readMacSynergyValues(file, sheet, nrow = 41, wellRangesExcel,
minThersholdForCVCal, minThersholdForCV, survivalFunc)
|
Arguments
file |
Name of fiele to be read |
sheet |
Sheet Number |
nrow |
Number of rows in the sheet |
wellRangesExcel |
TRUE if wells in excel formate |
minThersholdForCVCal |
Thresolld for data outliears in CV |
minThersholdForCV |
Thresold of values in CV not to remove |
survivalFunc |
<- function (x,y,z) (x-z)/(y-z) # It can be any function |
Value
Matrix of replicated values
Author(s)
Muhammad kashif
Examples
1 2 3 4 5 6 7 8 9 | fl <- system.file("extdata", "testData.csv", package="COMBIA")
sh <- 1
wellR <- list(c( "l3:l10","m3:m10","b3:k10", "l13:l20","m13:m20","b13:k20",
"l23:l30","m23:m30","b23:k30", "l33:l40","m33:m40","b33:k40"))
minThersholdForCV <- 0.3
minThersholdForCVCal <- 0.1
survivalFunc <- function (x,y,z) {(x-z)/(y-z)}
rslt <- readMacSynergyValues(fl, sh, nrow=41, wellR,
minThersholdForCVCal, minThersholdForCV, survivalFunc)
|
Example output
Loading required package: hash
hash-3.0.1 provided by Decision Patterns
Loading required package: lattice
Loading required package: latticeExtra
Loading required package: RColorBrewer
Loading required package: oro.nifti
oro.nifti 0.9.1
[1] "Ratio between empty and control 215.34756097561"
[1] "CV for control: 1 : 2.30698484671909"
[1] "Ratio between empty and control 216.431571815718"
[1] "CV for control: 2 : 3.97477131010254"
[1] "Ratio between empty and control 212.255570117955"
[1] "CV for control: 3 : 6.4008999376604"
[1] "Ratio between empty and control 191.453473132372"
[1] "CV for control: 4 : 5.87005801002331"
[1] "Number of the variable datapoints before data removal= 22"
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,] 0.4959273 0.4544325 0.4527889 0.5141335 0.7657826 0.8754745 0.9742680
[2,] 0.5282520 0.4508880 0.4907902 0.5426933 0.7353865 0.9182928 0.9180664
[3,] 0.4939636 0.4681056 0.5032695 0.5585093 0.7629166 0.8590776 0.9670757
[4,] 0.5893432 0.5392455 0.5748920 0.6414779 0.8667800 0.9914462 1.0411311
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] 0.9653167 0.3883595 0.4311439 0.5377761 0.5499641 0.7446938 0.8205780
[2,] 0.8856867 0.4417552 0.5078481 0.5198489 0.6046601 0.7495008 0.8080710
[3,] 1.0026615 0.3025846 0.4016490 0.5368700 0.5787590 0.7088183 0.8592761
[4,] 0.9958504 0.4488219 0.5907471 0.5606334 0.6452214 0.7078161 0.8624584
[,15] [,16] [,17] [,18] [,19] [,20] [,21]
[1,] 0.9662776 0.9516621 0.3719992 0.4589335 0.5391416 0.5714069 0.6952844
[2,] 0.8874478 0.8987191 0.4345346 0.5168550 0.5483290 0.5782179 0.6729921
[3,] 0.9738752 0.9966561 0.3164069 0.4027905 0.5139402 0.5712646 0.7147492
[4,] 0.9743249 0.8783960 0.4989471 0.5837279 0.5916279 0.6235858 0.7095227
[,22] [,23] [,24] [,25] [,26] [,27] [,28]
[1,] 0.8367865 0.9272861 0.9249851 0.00000000 0.2005835 0.3076203 0.5062694
[2,] 0.8237954 0.8538857 0.8311670 0.08167886 0.2314255 0.0000000 0.3672844
[3,] 0.8314577 0.9330037 0.9559334 0.06050699 0.0000000 0.1937179 0.4452006
[4,] 0.8354551 0.8611646 0.8680737 0.05142586 0.0000000 0.1851207 0.6040147
[,29] [,30] [,31] [,32] [,33] [,34] [,35]
[1,] 0.4562531 0.6521713 0.6713130 0.7385240 0.05020593 0.05465631 0.06740060
[2,] 0.4803995 0.5218113 0.6356309 0.6285863 0.03475723 0.05490963 0.06658343
[3,] 0.4499404 0.6100268 0.6939040 0.8689294 0.02834578 0.04132442 0.06430379
[4,] 0.4855143 0.5217113 0.6216590 0.6994481 0.03135924 0.05079276 0.00000000
[,36] [,37] [,38] [,39] [,40] [,41] [,42]
[1,] 0.12429475 0.1606059 0.2181069 0.2718402 0.3368766 0.02754941 0.04739915
[2,] 0.08167886 0.1406768 0.2105184 0.2518295 0.3291433 0.03548684 0.04884630
[3,] 0.08065737 0.1508611 0.1835683 0.2876951 0.3136276 0.03569124 0.04281336
[4,] 0.13160973 0.2082152 0.2306766 0.3238528 0.3092915 0.05068265 0.04264499
[,43] [,44] [,45] [,46] [,47] [,48] [,49]
[1,] 0.06808333 0.08942496 0.1572175 0.1623506 0.2106727 0.2543674 0.01933137
[2,] 0.07347701 0.11561843 0.1250531 0.1410291 0.2056878 0.2528611 0.03053051
[3,] 0.08353600 0.08701020 0.1579832 0.2060017 0.3179703 0.2390066 0.02948731
[4,] 0.11102012 0.08302596 0.1467216 0.1699538 0.2212626 0.2220058 0.04085579
[,50] [,51] [,52] [,53] [,54] [,55] [,56]
[1,] 0.03738578 0.06740060 0.09645455 0.1303635 0.1664470 0.1984847 0.2228354
[2,] 0.04690905 0.06693566 0.07219390 0.1162222 0.1463879 0.1632948 0.1580617
[3,] 0.05544457 0.08321339 0.11244634 0.1846601 0.1907400 0.2458806 0.2747413
[4,] 0.05445374 0.08222770 0.12626965 0.1550896 0.2057103 0.2272083 0.2090685
[,57] [,58] [,59] [,60] [,61] [,62] [,63]
[1,] 0.01025359 0.01930608 0.04671642 0.04841060 0.10983099 0.1492017 0.1828325
[2,] 0.03060599 0.03719766 0.05735006 0.04758835 0.10417106 0.1408530 0.1359973
[3,] 0.01926322 0.05350895 0.05651165 0.08440455 0.09614239 0.1644601 0.1522012
[4,] 0.02222054 0.04581051 0.04608577 0.06967574 0.11129538 0.1729541 0.1654670
[,64] [,65] [,66] [,67] [,68] [,69]
[1,] 0.0000000 -0.0005689415 0.001226385 0.006915800 0.001555107 0.007674388
[2,] 0.1718489 0.0030316658 0.001496964 0.002729757 0.015233806 0.041273425
[3,] 0.1958769 0.0100813956 0.008840608 0.015441596 0.042292230 0.029065439
[4,] 0.1998748 0.0032825016 0.011320157 0.007466487 0.002208979 0.045507721
[,70] [,71] [,72] [,73] [,74] [,75]
[1,] 0.005423909 0.03877652 0.00643536 0.000265506 0.0006700866 0.0003160786
[2,] 0.012994651 0.04655683 0.02595156 0.001673077 0.0009434645 0.0061765474
[3,] 0.012165918 0.04110107 0.02296077 0.002115542 0.0017184902 0.0017184902
[4,] 0.019302761 0.02464285 0.09648628 0.001135457 0.0005849321 0.0001720389
[,76] [,77] [,78] [,79] [,80]
[1,] -2.149334e-04 0.0003919375 -0.0002402197 0.0016056793 0.0011758124
[2,] 5.157606e-04 0.0005157606 0.0001383748 0.0020756218 0.0010189416
[3,] -1.861181e-05 0.0013958855 0.0001799141 0.0007258605 0.0001302827
[4,] 1.720389e-04 0.0014657711 0.0008601943 0.0012730876 -0.0002959069
[1] "Number of the variable datapoints after data removal= 17"
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