Nothing
tests/tPlotLinear.R
In Anaquin: Statistical analysis of sequins
#
# Copyright (C) 2016 - Garvan Institute of Medical Research
#
# Ted Wong, Bioinformatic Software Engineer at Garvan Institute
#
library(RUnit)
library(Anaquin)
.test.data <- function()
{
input <- c(15.1062,
15.1062,
966.797,
241.699,
30.2124,
7734.38,
483.398,
30937.5,
483.398,
15.1062,
483.398,
241.699,
60.4248,
0.118017,
7734.37,
7734.38,
120.85,
1933.59,
0.944138,
120.85,
7.5531,
3.77655,
3867.19,
15468.8,
1.88828,
1933.59,
120.85,
3867.19,
30.2124,
0.472069,
241.699,
60.4248,
0.944138,
120.85,
1.88828,
60.4248,
15468.8,
60.4248,
1933.59,
1.88828,
30.2124,
0.944138,
3867.19,
15468.8,
3867.19,
30.2124,
15.1062,
1933.59,
7.5531,
0.472069,
0.472069,
0.236034,
0.0590086,
241.699,
0.236034,
0.472069,
0.118017,
120.85,
0.118017,
483.398,
30937.5,
7.5531,
0.472069,
483.398,
7.5531,
966.797,
3.77655,
30937.5,
3.77655,
3.77655,
966.797,
3.77655,
0.236034,
1.88828,
0.0590086)
o1 <- c(4.29354,
6.41774,
271.696,
67.3212,
3.1943,
2628.81,
245.034,
14727.4,
38.2906,
8.41748,
140.367,
90.1342,
5.03172,
0.282232,
2340.3,
5418.16,
124.648,
157.443,
0.437077,
2.42797,
3.88121,
NA,
2010.24,
7762.18,
2.05478,
526.579,
29.9481,
1369.19,
9.21093,
0.305795,
50.4639,
11.4579,
0.291139,
76.4986,
3.2669,
21.1347,
8064.47,
37.4146,
438.561,
0.38055,
11.2435,
0.88877,
1491.72,
4786.46,
867.185,
7.30535,
2.78194,
559.819,
3.69124,
0.523401,
0.474327,
0.929315,
0.722466,
111.985,
1.1903,
1.47662,
0.285894,
35.2424,
0.700978,
419.301,
25760.2,
2.5859,
1.31373,
24.5161,
4.35937,
457.339,
2.59279,
15205,
0.64947,
1.1555,
261.917,
0.252222,
0.443106,
0.376111,
1.0948)
o2 <- c(3.09828,
8.68183,
272.248,
80.5532,
3.17143,
2813.75,
252.489,
15776.6,
55.5334,
7.92421,
134.694,
92.8906,
8.70729,
0.88829,
2313.62,
5647.12,
121.991,
157.827,
0.411342,
2.28061,
2.82815,
2.02179,
2007.42,
8399.07,
1.32179,
479.284,
30.1469,
1354.44,
7.04809,
0.688492,
45.6092,
16.2209,
0.655503,
64.66,
2.49032,
23.6616,
8801.15,
37.5889,
402.614,
0.792792,
13.1838,
1.30589,
1546.73,
5024.49,
870.876,
6.57147,
3.05968,
568.894,
3.72397,
0.650601,
NA,
0.970407,
0.902928,
107.726,
NA,
1.74165,
0.15758,
42.8825,
0.632109,
436.377,
27119.4,
4.50098,
0.297246,
18.5351,
2.64522,
490.524,
1.45904,
15831,
0.729047,
0.449076,
277.903,
2.34995,
0.385306,
0.864491,
0.944744)
o3 <- c(5.78108,
8.41477,
261.53,
71.0515,
2.22543,
2554.46,
235.358,
14074.1,
52.9666,
5.93463,
130.117,
89.6172,
13.3467,
2.71212,
2186.4,
5142.73,
122.094,
202.948,
3.26205,
3.628,
2.82539,
1.14586,
1921.63,
7459.34,
0.987163,
469.363,
27.2883,
1303.06,
10.1981,
1.0284,
44.2452,
14.9583,
1.95817,
62.0998,
4.66003,
24.9048,
7705.65,
39.1692,
377.697,
1.70661,
12.2224,
2.68944,
1432.93,
4672.95,
821.054,
6.00481,
2.91698,
549.193,
6.69091,
2.97898,
1.91727,
3.08212,
2.09839,
113.618,
2.05095,
4.40774,
1.82189,
36.1417,
4.30722,
410.602,
23843.5,
6.58454,
1.3233,
22.6614,
6.2324,
443.329,
1.81664,
14447.8,
2.18542,
0.148822,
237.506,
2.7184,
2.3283,
2.68241,
3.31801)
return (data.frame(Input=input, Observed1=o1, Observed2=o2, Observed3=o3))
}
test.PlotLinear_1 <- function()
{
x <- .test.data()
r <- plotLinear(row.names(x),
log2(x$Input),
log2(x$Observed1))
checkEqualsNumeric(r$LOQ$model$breaks, 0.9170727)
}
test.PlotLinear_2 <- function()
{
x <- .test.data()
r <- plotLinear(row.names(x),
log2(x$Input),
log2(x[,c(2:4)]))
checkEqualsNumeric(r$LOQ$model$breaks, 1.917068888)
}
test.PlotLinear_3 <- function()
{
x <- "15.1062,
15.1062,
241.699,
0.472069,
120.85,
483.398,
0.0590086,
483.398,
15.1062,
241.699,
60.4248,
120.85,
120.85,
0.472069,
0.118017,
0.0590086,
0.944138,
0.118017,
7.5531,
3.77655,
0.236034,
60.4248,
1.88828,
241.699,
0.118017,
0.236034,
0.472069,
30.2124,
241.699,
60.4248,
0.944138,
0.944138,
0.118017,
1.88828,
60.4248,
60.4248,
0.944138,
1.88828,
0.472069,
0.944138,
15.1062,
7.5531,
15.1062,
0.472069,
15.1062,
60.4248,
7.5531,
30.2124,
30.2124,
0.0590086,
0.236034,
0.0590086,
241.699,
0.236034,
30.2124,
120.85,
0.118017,
120.85,
1.88828,
7.5531,
30.2124,
483.398,
7.5531,
966.797,
3.77655,
241.699,
3.77655,
3.77655,
3.77655,
0.236034,
1.88828,
0.0590086"
y <- "2292.02,
1728.11,
33095.9,
51.557,
13616.2,
54615.3,
5.75489,
60652.2,
1205.27,
30255,
7645.25,
11118.4,
16529.2,
48.5283,
12.6669,
8.29854,
96.6785,
14.3095,
1151.03,
481.086,
22.5602,
9128.84,
203.783,
24093.9,
15.2307,
22.7496,
50.3159,
4104.9,
19207.5,
6752.21,
123.603,
187.043,
14.0419,
263.462,
3310.3,
8270.03,
119.862,
280.256,
1e-05,
115.157,
2042.86,
1084.78,
1773.62,
54.5923,
1733.97,
6365.94,
901.141,
4224.51,
3612.83,
14.9924,
29.9387,
5.04516,
30960.8,
35.6649,
3664.05,
17094.3,
13.5061,
13986.2,
248.781,
918.314,
3502.82,
64966.4,
860.103,
3426.51,
515.013,
32569.1,
609.002,
427.186,
677.121,
25.5264,
199.22,
8.10828"
z <- "R1_101,
R1_102,
R1_11,
R1_12,
R1_13,
R1_14,
R1_21,
R1_22,
R1_23,
R1_31,
R1_32,
R1_33,
R1_41,
R1_42,
R1_43,
R1_51,
R1_52,
R1_53,
R1_61,
R1_62,
R1_63,
R1_71,
R1_72,
R1_73,
R1_81,
R1_82,
R1_83,
R1_91,
R1_92,
R1_93,
R2_1,
R2_105,
R2_115,
R2_116,
R2_117,
R2_140,
R2_143,
R2_151,
R2_152,
R2_153,
R2_154,
R2_18,
R2_19,
R2_20,
R2_24,
R2_26,
R2_27,
R2_28,
R2_32,
R2_33,
R2_37,
R2_38,
R2_41,
R2_42,
R2_45,
R2_46,
R2_47,
R2_53,
R2_55,
R2_57,
R2_59,
R2_6,
R2_60,
R2_63,
R2_65,
R2_66,
R2_67,
R2_68,
R2_71,
R2_72,
R2_73,
R2_76"
r <- plotLinear(unlist(strsplit(z, split=',')),
log2(as.numeric(unlist(strsplit(x, split=',')))),
log2(as.numeric(unlist(strsplit(y, split=',')))),
showLOQ=TRUE)
checkEquals(NULL, r$LOQ)
}
test.PlotLinear_4 <- function()
{
x <- "10.0708,
5.0354,
0.8886,
14.2176,
107.422,
859.375,
161.133,
80.5664,
1.7772,
28.4352,
5156.25,
2578.12,
483.398,
3437.5,
27500,
53.7109,
429.688,
0.8886,
14.2176,
483.398,
26.8555,
214.844,
3.5544,
56.8704,
0.0786781,
0.0393391,
454.963,
7279.41,
5156.25,
2578.12,
13.4277,
107.422,
966.797,
966.797,
0.629425,
0.314713,
120.85,
0.4443,
7.1088,
2.5177,
1.25885,
227.482,
3639.71,
7734.38,
7734.38,
1.25885,
0.629425,
1289.06,
644.531,
60.4248,
60.4248,
3750,
117.188,
20.1416,
10.0708,
0.0143051,
0.457764,
120.85,
120.85,
30.2124,
30.2124,
80.5664,
40.2832,
0.269754,
0.539507,
1.07901,
30.2124,
30.2124,
60.4248,
2209.82,
4419.64,
8839.29,
58.5938,
1875,
0.269754,
0.539507,
1.07901,
15.1062,
15.1062,
0.134877,
0.269754,
0.539507,
1933.59,
1933.59,
7734.38,
7734.38,
2578.12,
1289.06,
0.944138,
20.1416,
10.0708,
1.67847,
13.4277,
1875,
58.5938,
0.839233,
6.71387,
0.0674384,
0.134877,
0.269754,
0.0674384,
0.134877,
0.269754,
0.0674384,
0.134877,
161.133,
80.5664,
0.0337192,
0.134877,
0.0314713,
0.0629425,
0.125885,
0.25177,
0.0168596,
0.0674384,
80.5664,
40.2832,
0.0168596,
0.0337192,
0.0674384,
322.266,
161.133,
937.5,
30000,
0.4443,
7.1088,
0.134877,
0.269754,
0.4443,
7.1088,
29.2969,
937.5,
3.77655,
937.5,
30000,
3.77655,
0.114441,
3.66211,
28.4352,
454.963,
0.114441,
3.66211,
0.0157356,
0.0314713,
0.0629425,
0.125885,
0.0572205,
1.83105,
29.2969,
937.5"
y1 <- "0.837485,
0.121353,
0.0379273,
0.768669,
1.90631,
0.744164,
1.0572e-06,
3.87601,
8.51e-08,
0.779118,
214.214,
1091.49,
54.3986,
380.045,
0.15194,
2.09719,
17.9671,
0.0795291,
0.478201,
3.56595,
2.38232,
15.8246,
0.394103,
0.895861,
8.8e-09,
0.0712489,
35.6487,
614.35,
988.259,
178.257,
0.532468,
3.26565,
44.7566,
41.5003,
0.0639191,
NA,
4.2057,
4.25e-08,
0.596072,
0.232307,
0.0675099,
2.28788,
423.966,
3907.65,
3567.12,
0.111393,
3.9771e-06,
133.993,
154.723,
4.34212,
0.996274,
85.0451,
4.61353,
0.163091,
0.379198,
NA,
0.038774,
3.21766,
15.0352,
1.38579,
1.93683,
9.35673,
5.451,
5e-08,
0.0649624,
0.384407,
3.77595,
7.44824,
16.0071,
270.303,
3.494e-07,
1671.87,
6.812,
325.095,
3.935e-07,
0.0616513,
0.0305549,
0.149523,
0.726862,
0.103768,
1.596e-06,
0.0463446,
199.256,
322.444,
1093.72,
1688.88,
279.584,
63.5678,
0.110435,
1.93013,
0.374583,
0.218183,
1.74819,
85.852,
1.21e-08,
0.377331,
1.96912,
NA,
NA,
NA,
0.130965,
1.18e-08,
2.91e-08,
NA,
NA,
15.1834,
9.38777,
NA,
0.0799122,
2.10385e-05,
NA,
0.083846,
NA,
0.0171778,
NA,
3.35384,
5.73421,
5.8264e-06,
6.246e-07,
0.0200194,
17.5116,
11.0122,
260.919,
3964.2,
0.100965,
1.11491,
0.0259428,
NA,
0.288957,
0.4821,
1.20828,
193.558,
0.536125,
187.495,
7064.26,
0.264505,
0.0221402,
0.396147,
3.55531,
73.5915,
NA,
NA,
9.9647e-06,
4.63e-08,
4.7e-09,
0.0237112,
0.0392847,
0.0456551,
1.70831,
91.1479"
y2 <- "0.722778,
0.733873,
5.219e-07,
0.604539,
1.73717,
1.1534,
1.9165e-06,
3.91994,
4.754e-07,
0.898643,
207.593,
1121.36,
54.4085,
373.338,
0.169796,
2.09949,
16.8435,
0.0616389,
0.619896,
3.89005,
2.5968,
16.6549,
0.182859,
0.948602,
1.016e-07,
0.0403375,
39.1606,
609.005,
1008.73,
157.116,
0.234875,
3.39922,
42.6545,
40.196,
0.181165,
2.847e-07,
4.69883,
NA,
0.189675,
0.254871,
0.391466,
2.41451,
426.951,
3810.71,
3577.81,
0.0420185,
4.103e-06,
120.872,
150.976,
4.00902,
1.09308,
88.7421,
4.36902,
0.325112,
0.487459,
0.0794166,
7.003e-07,
3.75052,
13.7295,
1.36716,
2.148,
8.88517,
5.73348,
0.00058588,
0.351373,
0.329472,
4.29572,
7.05352,
18.2358,
266.712,
3.379e-07,
1650,
6.13767,
312.299,
NA,
0.0414129,
NA,
0.158325,
1.03642,
0.0698399,
2.7166e-06,
0.0904658,
195.812,
309.716,
1161.1,
1716.5,
275.204,
61.8612,
NA,
1.05298,
0.427896,
3.555e-07,
2.10418,
80.0865,
1.96e-08,
0.512922,
1.58903,
6.00372e-05,
0.0432046,
NA,
2.8e-06,
1e-10,
0.0702308,
NA,
NA,
15.5818,
8.15287,
NA,
0.089151,
0.0283771,
1.102e-07,
1.27e-08,
3.0816e-06,
NA,
0.0412629,
3.26266,
7.27648,
NA,
NA,
NA,
17.6655,
10.9249,
249.933,
3641.64,
0.0509423,
0.640191,
0.0444007,
9.7502e-06,
0.319625,
0.436569,
1.04639,
191.152,
0.279646,
167.877,
7014.58,
0.392405,
2.306e-07,
0.334322,
2.50338,
65.9721,
0.0358907,
0.350269,
3.09e-08,
2.8e-09,
0.0405143,
9.942e-07,
NA,
0.010433,
1.02221,
95.2976"
y3 <- "0.490311,
0.469879,
0.16225,
0.490533,
2.13129,
1.0798,
2.2654e-06,
4.24638,
0.110956,
0.62222,
262.925,
1096.04,
48.0564,
399.27,
0.14716,
3.38397,
18.2888,
3.547e-07,
0.761565,
4.13325,
1.7191,
17.8298,
0.088615,
1.34844,
NA,
NA,
43.9125,
605.221,
1007.06,
177.07,
0.554892,
3.52786,
40.612,
46.9536,
2.0762e-06,
0.0886553,
4.04549,
0.060803,
0.413782,
0.11363,
NA,
2.72187,
429.049,
3861.91,
3759.93,
0.108981,
3.9713e-06,
121.845,
146.047,
4.52467,
1.6103,
93.0103,
5.10038,
0.51797,
0.195218,
2.26379e-05,
0.0758392,
3.94007,
11.767,
1.5896,
2.04017,
9.66727,
6.0005,
0.000148475,
0.165744,
0.127973,
3.72053,
6.65285,
16.6536,
279.149,
2.128e-07,
1707.2,
7.94687,
298.357,
NA,
0.0357967,
NA,
0.156696,
0.911175,
NA,
0.0614663,
0.0476663,
197.844,
317.099,
1223.97,
1618.46,
277.503,
66.3776,
0.072033,
1.72695,
0.216182,
0.172833,
1.6133,
89.5909,
2.87e-08,
0.496378,
1.83563,
1.506e-07,
NA,
0.137899,
NA,
NA,
NA,
0.0146193,
0.0325043,
14.8062,
7.7748,
0.0247236,
NA,
4.48882e-05,
NA,
0.0305807,
0.0408539,
0.0168537,
NA,
3.43573,
7.86324,
NA,
NA,
0.0196412,
17.5211,
11.9901,
253.366,
3609.29,
9.812e-07,
0.907263,
0.0254687,
NA,
0.208575,
0.40283,
0.836432,
191.248,
0.483889,
197.458,
6854.51,
0.171308,
4.1e-08,
0.303812,
1.92317,
67.3608,
NA,
NA,
NA,
NA,
NA,
NA,
NA,
0.0269071,
2.66745,
97.6445"
z <- "R1_101_1,
R1_101_2,
R1_102_1,
R1_102_2,
R1_103_1,
R1_103_2,
R1_11_1,
R1_11_2,
R1_12_1,
R1_12_2,
R1_13_1,
R1_13_2,
R1_14_1,
R1_21_1,
R1_21_2,
R1_22_1,
R1_22_2,
R1_23_1,
R1_23_2,
R1_24_1,
R1_31_1,
R1_31_2,
R1_32_1,
R1_32_2,
R1_33_1,
R1_33_2,
R1_41_1,
R1_41_2,
R1_42_1,
R1_42_2,
R1_43_1,
R1_43_2,
R1_51_1,
R1_51_2,
R1_52_1,
R1_52_2,
R1_53_1,
R1_61_1,
R1_61_2,
R1_62_1,
R1_62_2,
R1_63_1,
R1_63_2,
R1_71_1,
R1_71_2,
R1_72_1,
R1_72_2,
R1_73_1,
R1_73_2,
R1_81_1,
R1_81_2,
R1_82_1,
R1_82_2,
R1_83_1,
R1_83_2,
R1_91_1,
R1_91_2,
R1_92_1,
R1_92_2,
R1_93_1,
R1_93_2,
R2_115_1,
R2_115_2,
R2_116_1,
R2_116_2,
R2_116_3,
R2_117_1,
R2_117_3,
R2_140_1,
R2_14_1,
R2_14_2,
R2_14_3,
R2_150_1,
R2_150_2,
R2_151_1,
R2_151_2,
R2_151_3,
R2_152_1,
R2_152_2,
R2_153_1,
R2_153_2,
R2_153_3,
R2_154_1,
R2_154_2,
R2_18_1,
R2_18_2,
R2_19_1,
R2_19_2,
R2_1_1,
R2_20_1,
R2_20_2,
R2_24_1,
R2_24_2,
R2_26_1,
R2_26_2,
R2_27_1,
R2_27_2,
R2_28_1,
R2_28_2,
R2_28_3,
R2_32_1,
R2_32_2,
R2_32_3,
R2_37_2,
R2_37_3,
R2_41_1,
R2_41_2,
R2_42_1,
R2_42_3,
R2_45_1,
R2_45_2,
R2_45_3,
R2_45_4,
R2_46_1,
R2_46_3,
R2_47_1,
R2_47_2,
R2_53_1,
R2_53_2,
R2_53_3,
R2_54_1,
R2_54_2,
R2_55_2,
R2_55_3,
R2_57_1,
R2_57_2,
R2_59_2,
R2_59_3,
R2_60_1,
R2_60_2,
R2_63_1,
R2_63_3,
R2_65_1,
R2_66_1,
R2_66_2,
R2_67_1,
R2_68_1,
R2_68_2,
R2_6_1,
R2_6_2,
R2_71_1,
R2_71_2,
R2_72_1,
R2_72_2,
R2_72_3,
R2_72_4,
R2_73_1,
R2_73_2,
R2_7_1,
R2_7_2"
x <- log2(suppressWarnings(as.numeric(unlist(strsplit(x, split=',')))))
y1 <- log2(suppressWarnings(as.numeric(unlist(strsplit(y1, split=',')))))
y2 <- log2(suppressWarnings(as.numeric(unlist(strsplit(y2, split=',')))))
y3 <- log2(suppressWarnings(as.numeric(unlist(strsplit(y3, split=',')))))
z <- unlist(strsplit(z, split=','))
r <- plotLinear(c(z),
x,
data.frame(y1=y1, y2=y2, y3=y3),
showLOQ=TRUE, showSD=TRUE)
checkEqualsNumeric(0.8296060465, r$LOQ$model$breaks)
}
test.PlotLinear_1()
test.PlotLinear_2()
test.PlotLinear_3()
test.PlotLinear_4()
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Anaquin documentation built on Nov. 8, 2020, 5:23 p.m.
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#
# Copyright (C) 2016 - Garvan Institute of Medical Research
#
# Ted Wong, Bioinformatic Software Engineer at Garvan Institute
#
library(RUnit)
library(Anaquin)
.test.data <- function()
{
input <- c(15.1062,
15.1062,
966.797,
241.699,
30.2124,
7734.38,
483.398,
30937.5,
483.398,
15.1062,
483.398,
241.699,
60.4248,
0.118017,
7734.37,
7734.38,
120.85,
1933.59,
0.944138,
120.85,
7.5531,
3.77655,
3867.19,
15468.8,
1.88828,
1933.59,
120.85,
3867.19,
30.2124,
0.472069,
241.699,
60.4248,
0.944138,
120.85,
1.88828,
60.4248,
15468.8,
60.4248,
1933.59,
1.88828,
30.2124,
0.944138,
3867.19,
15468.8,
3867.19,
30.2124,
15.1062,
1933.59,
7.5531,
0.472069,
0.472069,
0.236034,
0.0590086,
241.699,
0.236034,
0.472069,
0.118017,
120.85,
0.118017,
483.398,
30937.5,
7.5531,
0.472069,
483.398,
7.5531,
966.797,
3.77655,
30937.5,
3.77655,
3.77655,
966.797,
3.77655,
0.236034,
1.88828,
0.0590086)
o1 <- c(4.29354,
6.41774,
271.696,
67.3212,
3.1943,
2628.81,
245.034,
14727.4,
38.2906,
8.41748,
140.367,
90.1342,
5.03172,
0.282232,
2340.3,
5418.16,
124.648,
157.443,
0.437077,
2.42797,
3.88121,
NA,
2010.24,
7762.18,
2.05478,
526.579,
29.9481,
1369.19,
9.21093,
0.305795,
50.4639,
11.4579,
0.291139,
76.4986,
3.2669,
21.1347,
8064.47,
37.4146,
438.561,
0.38055,
11.2435,
0.88877,
1491.72,
4786.46,
867.185,
7.30535,
2.78194,
559.819,
3.69124,
0.523401,
0.474327,
0.929315,
0.722466,
111.985,
1.1903,
1.47662,
0.285894,
35.2424,
0.700978,
419.301,
25760.2,
2.5859,
1.31373,
24.5161,
4.35937,
457.339,
2.59279,
15205,
0.64947,
1.1555,
261.917,
0.252222,
0.443106,
0.376111,
1.0948)
o2 <- c(3.09828,
8.68183,
272.248,
80.5532,
3.17143,
2813.75,
252.489,
15776.6,
55.5334,
7.92421,
134.694,
92.8906,
8.70729,
0.88829,
2313.62,
5647.12,
121.991,
157.827,
0.411342,
2.28061,
2.82815,
2.02179,
2007.42,
8399.07,
1.32179,
479.284,
30.1469,
1354.44,
7.04809,
0.688492,
45.6092,
16.2209,
0.655503,
64.66,
2.49032,
23.6616,
8801.15,
37.5889,
402.614,
0.792792,
13.1838,
1.30589,
1546.73,
5024.49,
870.876,
6.57147,
3.05968,
568.894,
3.72397,
0.650601,
NA,
0.970407,
0.902928,
107.726,
NA,
1.74165,
0.15758,
42.8825,
0.632109,
436.377,
27119.4,
4.50098,
0.297246,
18.5351,
2.64522,
490.524,
1.45904,
15831,
0.729047,
0.449076,
277.903,
2.34995,
0.385306,
0.864491,
0.944744)
o3 <- c(5.78108,
8.41477,
261.53,
71.0515,
2.22543,
2554.46,
235.358,
14074.1,
52.9666,
5.93463,
130.117,
89.6172,
13.3467,
2.71212,
2186.4,
5142.73,
122.094,
202.948,
3.26205,
3.628,
2.82539,
1.14586,
1921.63,
7459.34,
0.987163,
469.363,
27.2883,
1303.06,
10.1981,
1.0284,
44.2452,
14.9583,
1.95817,
62.0998,
4.66003,
24.9048,
7705.65,
39.1692,
377.697,
1.70661,
12.2224,
2.68944,
1432.93,
4672.95,
821.054,
6.00481,
2.91698,
549.193,
6.69091,
2.97898,
1.91727,
3.08212,
2.09839,
113.618,
2.05095,
4.40774,
1.82189,
36.1417,
4.30722,
410.602,
23843.5,
6.58454,
1.3233,
22.6614,
6.2324,
443.329,
1.81664,
14447.8,
2.18542,
0.148822,
237.506,
2.7184,
2.3283,
2.68241,
3.31801)
return (data.frame(Input=input, Observed1=o1, Observed2=o2, Observed3=o3))
}
test.PlotLinear_1 <- function()
{
x <- .test.data()
r <- plotLinear(row.names(x),
log2(x$Input),
log2(x$Observed1))
checkEqualsNumeric(r$LOQ$model$breaks, 0.9170727)
}
test.PlotLinear_2 <- function()
{
x <- .test.data()
r <- plotLinear(row.names(x),
log2(x$Input),
log2(x[,c(2:4)]))
checkEqualsNumeric(r$LOQ$model$breaks, 1.917068888)
}
test.PlotLinear_3 <- function()
{
x <- "15.1062,
15.1062,
241.699,
0.472069,
120.85,
483.398,
0.0590086,
483.398,
15.1062,
241.699,
60.4248,
120.85,
120.85,
0.472069,
0.118017,
0.0590086,
0.944138,
0.118017,
7.5531,
3.77655,
0.236034,
60.4248,
1.88828,
241.699,
0.118017,
0.236034,
0.472069,
30.2124,
241.699,
60.4248,
0.944138,
0.944138,
0.118017,
1.88828,
60.4248,
60.4248,
0.944138,
1.88828,
0.472069,
0.944138,
15.1062,
7.5531,
15.1062,
0.472069,
15.1062,
60.4248,
7.5531,
30.2124,
30.2124,
0.0590086,
0.236034,
0.0590086,
241.699,
0.236034,
30.2124,
120.85,
0.118017,
120.85,
1.88828,
7.5531,
30.2124,
483.398,
7.5531,
966.797,
3.77655,
241.699,
3.77655,
3.77655,
3.77655,
0.236034,
1.88828,
0.0590086"
y <- "2292.02,
1728.11,
33095.9,
51.557,
13616.2,
54615.3,
5.75489,
60652.2,
1205.27,
30255,
7645.25,
11118.4,
16529.2,
48.5283,
12.6669,
8.29854,
96.6785,
14.3095,
1151.03,
481.086,
22.5602,
9128.84,
203.783,
24093.9,
15.2307,
22.7496,
50.3159,
4104.9,
19207.5,
6752.21,
123.603,
187.043,
14.0419,
263.462,
3310.3,
8270.03,
119.862,
280.256,
1e-05,
115.157,
2042.86,
1084.78,
1773.62,
54.5923,
1733.97,
6365.94,
901.141,
4224.51,
3612.83,
14.9924,
29.9387,
5.04516,
30960.8,
35.6649,
3664.05,
17094.3,
13.5061,
13986.2,
248.781,
918.314,
3502.82,
64966.4,
860.103,
3426.51,
515.013,
32569.1,
609.002,
427.186,
677.121,
25.5264,
199.22,
8.10828"
z <- "R1_101,
R1_102,
R1_11,
R1_12,
R1_13,
R1_14,
R1_21,
R1_22,
R1_23,
R1_31,
R1_32,
R1_33,
R1_41,
R1_42,
R1_43,
R1_51,
R1_52,
R1_53,
R1_61,
R1_62,
R1_63,
R1_71,
R1_72,
R1_73,
R1_81,
R1_82,
R1_83,
R1_91,
R1_92,
R1_93,
R2_1,
R2_105,
R2_115,
R2_116,
R2_117,
R2_140,
R2_143,
R2_151,
R2_152,
R2_153,
R2_154,
R2_18,
R2_19,
R2_20,
R2_24,
R2_26,
R2_27,
R2_28,
R2_32,
R2_33,
R2_37,
R2_38,
R2_41,
R2_42,
R2_45,
R2_46,
R2_47,
R2_53,
R2_55,
R2_57,
R2_59,
R2_6,
R2_60,
R2_63,
R2_65,
R2_66,
R2_67,
R2_68,
R2_71,
R2_72,
R2_73,
R2_76"
r <- plotLinear(unlist(strsplit(z, split=',')),
log2(as.numeric(unlist(strsplit(x, split=',')))),
log2(as.numeric(unlist(strsplit(y, split=',')))),
showLOQ=TRUE)
checkEquals(NULL, r$LOQ)
}
test.PlotLinear_4 <- function()
{
x <- "10.0708,
5.0354,
0.8886,
14.2176,
107.422,
859.375,
161.133,
80.5664,
1.7772,
28.4352,
5156.25,
2578.12,
483.398,
3437.5,
27500,
53.7109,
429.688,
0.8886,
14.2176,
483.398,
26.8555,
214.844,
3.5544,
56.8704,
0.0786781,
0.0393391,
454.963,
7279.41,
5156.25,
2578.12,
13.4277,
107.422,
966.797,
966.797,
0.629425,
0.314713,
120.85,
0.4443,
7.1088,
2.5177,
1.25885,
227.482,
3639.71,
7734.38,
7734.38,
1.25885,
0.629425,
1289.06,
644.531,
60.4248,
60.4248,
3750,
117.188,
20.1416,
10.0708,
0.0143051,
0.457764,
120.85,
120.85,
30.2124,
30.2124,
80.5664,
40.2832,
0.269754,
0.539507,
1.07901,
30.2124,
30.2124,
60.4248,
2209.82,
4419.64,
8839.29,
58.5938,
1875,
0.269754,
0.539507,
1.07901,
15.1062,
15.1062,
0.134877,
0.269754,
0.539507,
1933.59,
1933.59,
7734.38,
7734.38,
2578.12,
1289.06,
0.944138,
20.1416,
10.0708,
1.67847,
13.4277,
1875,
58.5938,
0.839233,
6.71387,
0.0674384,
0.134877,
0.269754,
0.0674384,
0.134877,
0.269754,
0.0674384,
0.134877,
161.133,
80.5664,
0.0337192,
0.134877,
0.0314713,
0.0629425,
0.125885,
0.25177,
0.0168596,
0.0674384,
80.5664,
40.2832,
0.0168596,
0.0337192,
0.0674384,
322.266,
161.133,
937.5,
30000,
0.4443,
7.1088,
0.134877,
0.269754,
0.4443,
7.1088,
29.2969,
937.5,
3.77655,
937.5,
30000,
3.77655,
0.114441,
3.66211,
28.4352,
454.963,
0.114441,
3.66211,
0.0157356,
0.0314713,
0.0629425,
0.125885,
0.0572205,
1.83105,
29.2969,
937.5"
y1 <- "0.837485,
0.121353,
0.0379273,
0.768669,
1.90631,
0.744164,
1.0572e-06,
3.87601,
8.51e-08,
0.779118,
214.214,
1091.49,
54.3986,
380.045,
0.15194,
2.09719,
17.9671,
0.0795291,
0.478201,
3.56595,
2.38232,
15.8246,
0.394103,
0.895861,
8.8e-09,
0.0712489,
35.6487,
614.35,
988.259,
178.257,
0.532468,
3.26565,
44.7566,
41.5003,
0.0639191,
NA,
4.2057,
4.25e-08,
0.596072,
0.232307,
0.0675099,
2.28788,
423.966,
3907.65,
3567.12,
0.111393,
3.9771e-06,
133.993,
154.723,
4.34212,
0.996274,
85.0451,
4.61353,
0.163091,
0.379198,
NA,
0.038774,
3.21766,
15.0352,
1.38579,
1.93683,
9.35673,
5.451,
5e-08,
0.0649624,
0.384407,
3.77595,
7.44824,
16.0071,
270.303,
3.494e-07,
1671.87,
6.812,
325.095,
3.935e-07,
0.0616513,
0.0305549,
0.149523,
0.726862,
0.103768,
1.596e-06,
0.0463446,
199.256,
322.444,
1093.72,
1688.88,
279.584,
63.5678,
0.110435,
1.93013,
0.374583,
0.218183,
1.74819,
85.852,
1.21e-08,
0.377331,
1.96912,
NA,
NA,
NA,
0.130965,
1.18e-08,
2.91e-08,
NA,
NA,
15.1834,
9.38777,
NA,
0.0799122,
2.10385e-05,
NA,
0.083846,
NA,
0.0171778,
NA,
3.35384,
5.73421,
5.8264e-06,
6.246e-07,
0.0200194,
17.5116,
11.0122,
260.919,
3964.2,
0.100965,
1.11491,
0.0259428,
NA,
0.288957,
0.4821,
1.20828,
193.558,
0.536125,
187.495,
7064.26,
0.264505,
0.0221402,
0.396147,
3.55531,
73.5915,
NA,
NA,
9.9647e-06,
4.63e-08,
4.7e-09,
0.0237112,
0.0392847,
0.0456551,
1.70831,
91.1479"
y2 <- "0.722778,
0.733873,
5.219e-07,
0.604539,
1.73717,
1.1534,
1.9165e-06,
3.91994,
4.754e-07,
0.898643,
207.593,
1121.36,
54.4085,
373.338,
0.169796,
2.09949,
16.8435,
0.0616389,
0.619896,
3.89005,
2.5968,
16.6549,
0.182859,
0.948602,
1.016e-07,
0.0403375,
39.1606,
609.005,
1008.73,
157.116,
0.234875,
3.39922,
42.6545,
40.196,
0.181165,
2.847e-07,
4.69883,
NA,
0.189675,
0.254871,
0.391466,
2.41451,
426.951,
3810.71,
3577.81,
0.0420185,
4.103e-06,
120.872,
150.976,
4.00902,
1.09308,
88.7421,
4.36902,
0.325112,
0.487459,
0.0794166,
7.003e-07,
3.75052,
13.7295,
1.36716,
2.148,
8.88517,
5.73348,
0.00058588,
0.351373,
0.329472,
4.29572,
7.05352,
18.2358,
266.712,
3.379e-07,
1650,
6.13767,
312.299,
NA,
0.0414129,
NA,
0.158325,
1.03642,
0.0698399,
2.7166e-06,
0.0904658,
195.812,
309.716,
1161.1,
1716.5,
275.204,
61.8612,
NA,
1.05298,
0.427896,
3.555e-07,
2.10418,
80.0865,
1.96e-08,
0.512922,
1.58903,
6.00372e-05,
0.0432046,
NA,
2.8e-06,
1e-10,
0.0702308,
NA,
NA,
15.5818,
8.15287,
NA,
0.089151,
0.0283771,
1.102e-07,
1.27e-08,
3.0816e-06,
NA,
0.0412629,
3.26266,
7.27648,
NA,
NA,
NA,
17.6655,
10.9249,
249.933,
3641.64,
0.0509423,
0.640191,
0.0444007,
9.7502e-06,
0.319625,
0.436569,
1.04639,
191.152,
0.279646,
167.877,
7014.58,
0.392405,
2.306e-07,
0.334322,
2.50338,
65.9721,
0.0358907,
0.350269,
3.09e-08,
2.8e-09,
0.0405143,
9.942e-07,
NA,
0.010433,
1.02221,
95.2976"
y3 <- "0.490311,
0.469879,
0.16225,
0.490533,
2.13129,
1.0798,
2.2654e-06,
4.24638,
0.110956,
0.62222,
262.925,
1096.04,
48.0564,
399.27,
0.14716,
3.38397,
18.2888,
3.547e-07,
0.761565,
4.13325,
1.7191,
17.8298,
0.088615,
1.34844,
NA,
NA,
43.9125,
605.221,
1007.06,
177.07,
0.554892,
3.52786,
40.612,
46.9536,
2.0762e-06,
0.0886553,
4.04549,
0.060803,
0.413782,
0.11363,
NA,
2.72187,
429.049,
3861.91,
3759.93,
0.108981,
3.9713e-06,
121.845,
146.047,
4.52467,
1.6103,
93.0103,
5.10038,
0.51797,
0.195218,
2.26379e-05,
0.0758392,
3.94007,
11.767,
1.5896,
2.04017,
9.66727,
6.0005,
0.000148475,
0.165744,
0.127973,
3.72053,
6.65285,
16.6536,
279.149,
2.128e-07,
1707.2,
7.94687,
298.357,
NA,
0.0357967,
NA,
0.156696,
0.911175,
NA,
0.0614663,
0.0476663,
197.844,
317.099,
1223.97,
1618.46,
277.503,
66.3776,
0.072033,
1.72695,
0.216182,
0.172833,
1.6133,
89.5909,
2.87e-08,
0.496378,
1.83563,
1.506e-07,
NA,
0.137899,
NA,
NA,
NA,
0.0146193,
0.0325043,
14.8062,
7.7748,
0.0247236,
NA,
4.48882e-05,
NA,
0.0305807,
0.0408539,
0.0168537,
NA,
3.43573,
7.86324,
NA,
NA,
0.0196412,
17.5211,
11.9901,
253.366,
3609.29,
9.812e-07,
0.907263,
0.0254687,
NA,
0.208575,
0.40283,
0.836432,
191.248,
0.483889,
197.458,
6854.51,
0.171308,
4.1e-08,
0.303812,
1.92317,
67.3608,
NA,
NA,
NA,
NA,
NA,
NA,
NA,
0.0269071,
2.66745,
97.6445"
z <- "R1_101_1,
R1_101_2,
R1_102_1,
R1_102_2,
R1_103_1,
R1_103_2,
R1_11_1,
R1_11_2,
R1_12_1,
R1_12_2,
R1_13_1,
R1_13_2,
R1_14_1,
R1_21_1,
R1_21_2,
R1_22_1,
R1_22_2,
R1_23_1,
R1_23_2,
R1_24_1,
R1_31_1,
R1_31_2,
R1_32_1,
R1_32_2,
R1_33_1,
R1_33_2,
R1_41_1,
R1_41_2,
R1_42_1,
R1_42_2,
R1_43_1,
R1_43_2,
R1_51_1,
R1_51_2,
R1_52_1,
R1_52_2,
R1_53_1,
R1_61_1,
R1_61_2,
R1_62_1,
R1_62_2,
R1_63_1,
R1_63_2,
R1_71_1,
R1_71_2,
R1_72_1,
R1_72_2,
R1_73_1,
R1_73_2,
R1_81_1,
R1_81_2,
R1_82_1,
R1_82_2,
R1_83_1,
R1_83_2,
R1_91_1,
R1_91_2,
R1_92_1,
R1_92_2,
R1_93_1,
R1_93_2,
R2_115_1,
R2_115_2,
R2_116_1,
R2_116_2,
R2_116_3,
R2_117_1,
R2_117_3,
R2_140_1,
R2_14_1,
R2_14_2,
R2_14_3,
R2_150_1,
R2_150_2,
R2_151_1,
R2_151_2,
R2_151_3,
R2_152_1,
R2_152_2,
R2_153_1,
R2_153_2,
R2_153_3,
R2_154_1,
R2_154_2,
R2_18_1,
R2_18_2,
R2_19_1,
R2_19_2,
R2_1_1,
R2_20_1,
R2_20_2,
R2_24_1,
R2_24_2,
R2_26_1,
R2_26_2,
R2_27_1,
R2_27_2,
R2_28_1,
R2_28_2,
R2_28_3,
R2_32_1,
R2_32_2,
R2_32_3,
R2_37_2,
R2_37_3,
R2_41_1,
R2_41_2,
R2_42_1,
R2_42_3,
R2_45_1,
R2_45_2,
R2_45_3,
R2_45_4,
R2_46_1,
R2_46_3,
R2_47_1,
R2_47_2,
R2_53_1,
R2_53_2,
R2_53_3,
R2_54_1,
R2_54_2,
R2_55_2,
R2_55_3,
R2_57_1,
R2_57_2,
R2_59_2,
R2_59_3,
R2_60_1,
R2_60_2,
R2_63_1,
R2_63_3,
R2_65_1,
R2_66_1,
R2_66_2,
R2_67_1,
R2_68_1,
R2_68_2,
R2_6_1,
R2_6_2,
R2_71_1,
R2_71_2,
R2_72_1,
R2_72_2,
R2_72_3,
R2_72_4,
R2_73_1,
R2_73_2,
R2_7_1,
R2_7_2"
x <- log2(suppressWarnings(as.numeric(unlist(strsplit(x, split=',')))))
y1 <- log2(suppressWarnings(as.numeric(unlist(strsplit(y1, split=',')))))
y2 <- log2(suppressWarnings(as.numeric(unlist(strsplit(y2, split=',')))))
y3 <- log2(suppressWarnings(as.numeric(unlist(strsplit(y3, split=',')))))
z <- unlist(strsplit(z, split=','))
r <- plotLinear(c(z),
x,
data.frame(y1=y1, y2=y2, y3=y3),
showLOQ=TRUE, showSD=TRUE)
checkEqualsNumeric(0.8296060465, r$LOQ$model$breaks)
}
test.PlotLinear_1()
test.PlotLinear_2()
test.PlotLinear_3()
test.PlotLinear_4()
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