An R package for simulating omics datasets either from scratch or from existing, publicly available datasets. Configurable parameters are correlation structure, biases, noise and the relationship between predictors and outcome variable.
Evaluation of statistical methods is best done with datasets where all relevant parameters can be controlled. Parameters of interest are e.g. the number of observations/features, the correlation structure between samples/features, the relationship between features and outcome and the amount of noise and/or biases within the data. As this is rarely possible with real-world datasets, it often makes sense to not only evaluate methods on real-world datasets, but also on simulated datasets. The goal of this package is therefore, to make simulation of such datasets as easy as possible.
- Remove
gseparameter - Fix indentation of examples in README
- Fix simplest bias example in README
- Replace
*.csvfiles with one big.rdaor.rdsfile (see functionsaveRDS) - Read
*.rdsfile only once (see e.g. packagememoise) - Add a changelog to the package (from now on, every pull request should increase the package version. See https://keepachangelog.com/en/1.0.0/ and https://semver.org/.
- Make
list_datasetsreturn all available Metadata (not just title title, type, platform_id and data_row_count) - Document package usage either in a vignette or in chapter Usage.
- Write tests for all functions. See https://r-pkgs.org/tests.html for details on how to write testcases for R functions.
- Implement
cor_func/cor_func_argsargument: be creative - Make sure all functions are thoroughly documented. See https://r-pkgs.org/man.html for details on how to write documentation for R functions.
- Improve literature research results.
- Publish the package to CRAN.
- Optional: speed up
list_datasetsby retrieving the metadata without actually downloading the expression matrix (maybe by querying the NCBI website)
# From Github (development version)
devtools::install_github("toscm/simulatr")
# From CRAN (stable version)
install.packages("simulatr") # not yet availableGenerates a (5,5) dataframe with random data.
simulatr::simulate_dataset()
#result:
# $Raw_data
# X1 X2 X3 X4 X5
# 1 0.1762176 -0.31198363 0.32223354 -0.2343050 -0.05572341
# 2 1.1550628 1.99176568 1.13742129 -0.2090538 0.80900189
# 3 1.7199090 0.06935324 1.09140363 0.7656588 -0.36169380
# 4 -1.5826347 -0.78319329 -1.48307500 0.3422295 0.87223922
# 5 -1.9270000 -0.64069114 0.02274371 -1.0025085 1.26573656
# $Noise_matrix
# [,1] [,2] [,3] [,4] [,5]
# [1,] 0 0 0 0 0
# [2,] 0 0 0 0 0
# [3,] 0 0 0 0 0
# [4,] 0 0 0 0 0
# [5,] 0 0 0 0 0
# $Bias_matrix
# [,1] [,2] [,3] [,4] [,5]
# [1,] 0 0 0 0 0
# [2,] 0 0 0 0 0
# [3,] 0 0 0 0 0
# [4,] 0 0 0 0 0
# [5,] 0 0 0 0 0
# $Final_data
# X1 X2 X3 X4 X5
# 1 0.1762176 -0.31198363 0.32223354 -0.2343050 -0.05572341
# 2 1.1550628 1.99176568 1.13742129 -0.2090538 0.80900189
# 3 1.7199090 0.06935324 1.09140363 0.7656588 -0.36169380
# 4 -1.5826347 -0.78319329 -1.48307500 0.3422295 0.87223922
# 5 -1.9270000 -0.64069114 0.02274371 -1.0025085 1.26573656
The users can define the dimension of the simulated data. n is the number of
samples and p is the number of features (e.g. genes).
simulatr::simulate_dataset(n = 2, p = 3)
# result :
# $Raw_data
# X1 X2 X3
# 1 0.9534753 1.5397671 1.3401822
# 2 1.1404721 0.4871656 -0.5003632
# $Noise_matrix
# [,1] [,2] [,3]
# [1,] 0 0 0
# [2,] 0 0 0
# $Bias_matrix
# [,1] [,2] [,3]
# [1,] 0 0 0
# [2,] 0 0 0
# $Final_data
# X1 X2 X3
# 1 0.9534753 1.5397671 1.3401822
# 2 1.1404721 0.4871656 -0.5003632
The users can provide a dataframe from which they want to derive the simulated data.
The following simulated data is derived from normal distribution.
simulatr::simulate_dataset(n = 5,
p = 5,
base = data.frame(matrix(stats::rnorm(6 * 6), 6, 6)))
# result :
# X4 X5 X1 X2 X6
# 5 0.1256898 -0.3160537 0.04232887 1.18364610 0.02548396
# 3 -0.6574073 0.2382905 1.80930896 -0.80482068 1.40157078
# 1 1.9728739 -0.5976392 0.14674887 -1.29226331 0.48473688
# 6 -2.1417302 0.5517731 1.76103325 -0.22870073 0.66565249
# 4 0.2322724 -2.5704606 0.96798778 0.03665393 2.24897548
The user can get simulated data derived by generalised linear model using the following function.
simulatr::simulate_dataset(n = 5,
p = 6,
base = simulate_glm_data(dat = as.data.frame(simulatr::get_dataset(
gse = "GSE3821"
))))
# result :
# $Raw_data
# GSM87675 GSM87673 GSM87662 GSM87665 GSM87663 GSM87668
# 6417_at 0.4946612 -11.16338 0.5856437 3.0071917 28.81056 -0.69561632
# 5828_at 59.3605483 54.34398 121.6307257 120.9315708 158.00851 72.94667034
# 2909_at 0.3321056 -11.19807 1.6905615 0.5061987 28.47222 0.03810145
# 7983_at 300.2944299 284.08063 564.7004732 745.5949269 872.47721 299.40028589
# 6154_at 1525.4323096 1541.10006 2848.4504152 1795.9567249 3083.38419 1617.09406563
# $Noise_matrix
# [,1] [,2] [,3] [,4] [,5] [,6]
# [1,] 0 0 0 0 0 0
# [2,] 0 0 0 0 0 0
# [3,] 0 0 0 0 0 0
# [4,] 0 0 0 0 0 0
# [5,] 0 0 0 0 0 0
# $Bias_matrix
# [,1] [,2] [,3] [,4] [,5] [,6]
# [1,] 0 0 0 0 0 0
# [2,] 0 0 0 0 0 0
# [3,] 0 0 0 0 0 0
# [4,] 0 0 0 0 0 0
# [5,] 0 0 0 0 0 0
# $Final_data
# GSM87675 GSM87673 GSM87662 GSM87665 GSM87663 GSM87668
# 6417_at 0.4946612 -11.16338 0.5856437 3.0071917 28.81056 -0.69561632
# 5828_at 59.3605483 54.34398 121.6307257 120.9315708 158.00851 72.94667034
# 2909_at 0.3321056 -11.19807 1.6905615 0.5061987 28.47222 0.03810145
# 7983_at 300.2944299 284.08063 564.7004732 745.5949269 872.47721 299.40028589
# 6154_at 1525.4323096 1541.10006 2848.4504152 1795.9567249 3083.38419 1617.09406563
beta is a (q*p) matrix to denote the effect of each feature. y is the
response variable derived from the predictor variable base.
Suppose, we throw a ball. Here y is the height at time base. beta (for
this example, beta[1] is the initial velocity and beta[2] is the gravity) is
derived from the observed data base with the help of regression.
simulate_dataset(
n = 5,
p = 5,
base = data.frame(matrix(rnorm(5*5), 5, 5)),
beta = matrix(1, 1, 5),
noise_func = uniform_noise,
noise_func_args = list(min = 0, max = 0.5),
bias_func = constant_batch_effect,
bias_func_args = list(
b = 2,
f = 3,
s = c(2, 3)
)
)
# result :
# $Raw_data
# X1 X2 X3 X4 X5
# 1 -0.5631143 -1.25772826 -2.88727732 2.0029593 1.07202852
# 2 0.7342713 -0.22725993 0.49327326 -0.2374921 0.90956033
# 3 -0.6018707 0.04448858 0.39703575 -0.1720591 -0.23891208
# 4 -1.5804805 -0.45933286 -0.62823990 0.8727630 0.01172443
# 5 -0.1881927 0.03466649 0.04679791 -1.8362100 0.60073192
# $y
# [,1]
# [1,] -1.6331320
# [2,] 1.6723528
# [3,] -0.5713176
# [4,] -1.7835658
# [5,] -1.3422064
# $Noise_matrix
# [,1] [,2] [,3] [,4] [,5]
# [1,] 0.20522398 0.19019955 0.44916230 0.449675806 0.18695505
# [2,] 0.15800413 0.05544260 0.12167595 0.365121750 0.13632798
# [3,] 0.06898693 0.26681824 0.46568979 0.164445931 0.47057208
# [4,] 0.38260321 0.05597352 0.30260381 0.019969805 0.04433646
# [5,] 0.41993020 0.48683033 0.03221877 0.008465517 0.06728425
# $Bias_arguments
# $Bias_arguments$b
# [1] 1 2 2 2 1
# $Bias_arguments$f
# [1] 3
# $Bias_arguments$s
# [1] 2 3
# $Bias_matrix
# [,1] [,2] [,3] [,4] [,5]
# [1,] 2 2 0 2 0
# [2,] 3 3 0 3 0
# [3,] 3 3 0 3 0
# [4,] 3 3 0 3 0
# [5,] 2 2 0 2 0
# $Features_affected
# [1] 1 2 4
# $Final_data
# X1 X2 X3 X4 X5
# 1 1.642110 0.9324713 -2.43811502 4.4526351 1.25898356
# 2 3.892275 2.8281827 0.61494921 3.1276296 1.04588830
# 3 2.467116 3.3113068 0.86272554 2.9923868 0.23166000
# 4 1.802123 2.5966407 -0.32563608 3.8927328 0.05606089
# 5 2.231737 2.5214968 0.07901668 0.1722555 0.66801617
The users can use simulate_gse function as base. In that case, the users will
get simulated data related to that specific gse number.
simulatr::simulate_dataset(n = 5,
p = 5,
base = simulatr::simulate_gse(n = 10, p = 10, "GSE3821"))
# result :
# $Raw_data
# GSM87674 GSM87666 GSM87669 GSM87661 GSM87671
# 10858_s_at 4.6 368.7 317.8 132.2 0.9
# 6278_at 43.1 203.8 59.9 4.9 21.5
# 5267_at 3.5 1567.8 1635.4 110.1 162.1
# 3937_g_at 24.0 18.2 711.9 5.9 12.8
# 9673_at 65.2 2.8 129.3 107.7 88.7
# $Noise_matrix
# [,1] [,2] [,3] [,4] [,5]
# [1,] 0 0 0 0 0
# [2,] 0 0 0 0 0
# [3,] 0 0 0 0 0
# [4,] 0 0 0 0 0
# [5,] 0 0 0 0 0
# $Bias_matrix
# [,1] [,2] [,3] [,4] [,5]
# [1,] 0 0 0 0 0
# [2,] 0 0 0 0 0
# [3,] 0 0 0 0 0
# [4,] 0 0 0 0 0
# [5,] 0 0 0 0 0
# $Final_data
# GSM87674 GSM87666 GSM87669 GSM87661 GSM87671
# 10858_s_at 4.6 368.7 317.8 132.2 0.9
# 6278_at 43.1 203.8 59.9 4.9 21.5
# 5267_at 3.5 1567.8 1635.4 110.1 162.1
# 3937_g_at 24.0 18.2 711.9 5.9 12.8
# 9673_at 65.2 2.8 129.3 107.7 88.7
The users can choose the type of noise they want to add to their simulated data. They can either provide their own noise (a n*p dimensional matrix) or choose from the given noise functions. If they choose the given noise function, they have to provide arguments for the chosen one. We provide noise function with gaussian, poisson, exponential, binomial and uniform distribution.
Here argument sd is the standard deviation of the noise.
simulatr::simulate_dataset(n = 5,
p = 5,
noise_func = random_noise,
noise_func_args = list(sd = 1))
# result :
# $Raw_data
# X1 X2 X3 X4 X5
# 1 2.2311449 0.03653275 -0.5661968 -1.3128648 1.904511959
# 2 -1.1314648 0.45451584 0.6629861 0.3385688 -0.308275629
# 3 -0.4960574 -0.66998209 -0.8543475 -0.1887187 -0.395712112
# 4 0.4143783 2.02210645 -0.6322548 -0.3483600 0.990630383
# 5 -0.3332484 -1.57109667 -1.6374831 0.4433273 0.007154562
# $Noise_matrix
# [,1] [,2] [,3] [,4] [,5]
# [1,] 0.90979703 2.0057072 1.4083337 1.1825010 -0.6467732
# [2,] 0.79984495 -0.3275907 0.6731386 1.6362032 1.6661878
# [3,] 1.94676034 -0.6974455 2.2211487 -0.3635689 1.1419819
# [4,] 0.88901690 1.9337181 2.7419242 0.3615179 -0.1667313
# [5,] 0.05061772 -1.0825537 1.9258480 0.1851097 1.3866912
# $Bias_matrix
# [,1] [,2] [,3] [,4] [,5]
# [1,] 0 0 0 0 0
# [2,] 0 0 0 0 0
# [3,] 0 0 0 0 0
# [4,] 0 0 0 0 0
# [5,] 0 0 0 0 0
# $Final_data
# X1 X2 X3 X4 X5
# 1 3.1409419 2.0422400 0.8421368 -0.13036382 1.2577387
# 2 -0.3316198 0.1269251 1.3361247 1.97477198 1.3579122
# 3 1.4507030 -1.3674276 1.3668012 -0.55228759 0.7462698
# 4 1.3033952 3.9558245 2.1096693 0.01315786 0.8238991
# 5 -0.2826306 -2.6536504 0.2883648 0.62843704 1.3938458
Here lambda is the argument of poisson noise.
simulatr::simulate_dataset(n = 5,
p = 5,
noise_func = poisson_noise,
noise_func_args = list(lambda = 1))
# result :
# $Raw_data
# X1 X2 X3 X4 X5
# 1 -0.05811362 1.09581610 0.1266713 -0.1083199 0.5128394
# 2 -0.92454146 1.38474517 0.4271527 0.3935762 0.7285983
# 3 -0.54955544 -0.94320261 -0.4588501 1.7493039 0.3129103
# 4 0.14519516 -0.07714980 0.9755154 0.2408752 -2.7976624
# 5 0.65178727 0.09877979 -0.2932061 -1.0808705 -0.7367765
# $Noise_matrix
# [,1] [,2] [,3] [,4] [,5]
# [1,] 0 1 0 2 2
# [2,] 2 0 1 1 1
# [3,] 0 2 2 1 0
# [4,] 0 0 0 3 1
# [5,] 0 3 0 1 2
# $Bias_matrix
# [,1] [,2] [,3] [,4] [,5]
# [1,] 0 0 0 0 0
# [2,] 0 0 0 0 0
# [3,] 0 0 0 0 0
# [4,] 0 0 0 0 0
# [5,] 0 0 0 0 0
# $Final_data
# X1 X2 X3 X4 X5
# 1 -0.05811362 2.0958161 0.1266713 1.89168008 2.5128394
# 2 1.07545854 1.3847452 1.4271527 1.39357615 1.7285983
# 3 -0.54955544 1.0567974 1.5411499 2.74930391 0.3129103
# 4 0.14519516 -0.0771498 0.9755154 3.24087522 -1.7976624
# 5 0.65178727 3.0987798 -0.2932061 -0.08087049 1.2632235Here min and max are the function arguments of uniform noise. min and
max define the range of the noise.
simulatr::simulate_dataset(n = 5,
p = 5,
noise_func = uniform_noise,
noise_func_args = list(min = 1, max = 2))
# result :
# $Raw_data
# X1 X2 X3 X4 X5
# 1 -0.7797268 -0.996224433 0.36576369 -1.4733228 0.3948879
# 2 -1.4080089 0.105231072 1.52907588 0.2473507 -1.4453939
# 3 -0.3974147 0.002860514 -0.44420052 1.1363579 -0.6719359
# 4 -0.7413664 1.093064653 0.05801465 -1.1002725 -0.1508035
# 5 -0.3506015 -0.608807304 -0.93857778 -0.4832457 0.2615543
# $Noise_matrix
# [,1] [,2] [,3] [,4] [,5]
# [1,] 1.434359 1.453844 1.398531 1.733971 1.032687
# [2,] 1.562779 1.130768 1.363593 1.813566 1.528254
# [3,] 1.852378 1.208463 1.883415 1.395400 1.042114
# [4,] 1.471074 1.652778 1.102623 1.084424 1.153834
# [5,] 1.118819 1.485851 1.683057 1.599802 1.846646
# $Bias_matrix
# [,1] [,2] [,3] [,4] [,5]
# [1,] 0 0 0 0 0
# [2,] 0 0 0 0 0
# [3,] 0 0 0 0 0
# [4,] 0 0 0 0 0
# [5,] 0 0 0 0 0
# $Final_data
# X1 X2 X3 X4 X5
# 1 0.6546318 0.4576194 1.7642946 0.26064842 1.42757512
# 2 0.1547698 1.2359988 2.8926688 2.06091677 0.08285979
# 3 1.4549628 1.2113237 1.4392149 2.53175808 0.37017818
# 4 0.7297077 2.7458426 1.1606372 -0.01584851 1.00303089
# 5 0.7682178 0.8770436 0.7444793 1.11655609 2.10819990
Here size and prob are the function arguments. size defines the number of
trials and prob defines the probability of success on each trial.
simulatr::simulate_dataset(n = 5,
p = 5,
noise_func = binomial_noise,
noise_func_args = list(size = 10, prob = 0.5))
# result :
# $Raw_data
# X1 X2 X3 X4 X5
# 1 -0.99022351 -1.33748943 -1.06756227 2.1751393 1.2303136
# 2 -1.15137820 0.62407057 -0.70550466 0.4030568 -0.9331593
# 3 1.24113048 -0.05228867 0.06352701 1.5743568 -0.2792377
# 4 0.05258765 1.01758132 0.34715785 0.9336842 -0.6732322
# 5 -1.14486335 -0.84741043 -0.65201094 -1.1267899 2.0442877
# $Noise_matrix
# [,1] [,2] [,3] [,4] [,5]
# [1,] 6 5 4 7 7
# [2,] 4 5 6 4 4
# [3,] 3 5 6 4 3
# [4,] 6 5 4 7 7
# [5,] 5 5 5 4 5
# $Bias_matrix
# [,1] [,2] [,3] [,4] [,5]
# [1,] 0 0 0 0 0
# [2,] 0 0 0 0 0
# [3,] 0 0 0 0 0
# [4,] 0 0 0 0 0
# [5,] 0 0 0 0 0
# $Final_data
# X1 X2 X3 X4 X5
# 1 5.009776 3.662511 2.932438 9.175139 8.230314
# 2 2.848622 5.624071 5.294495 4.403057 3.066841
# 3 4.241130 4.947711 6.063527 5.574357 2.720762
# 4 6.052588 6.017581 4.347158 7.933684 6.326768
# 5 3.855137 4.152590 4.347989 2.873210 7.044288
Here rate is the function argument.
simulatr::simulate_dataset(n = 5,
p = 5,
noise_func = exponential_noise,
noise_func_args = list(rate = 1))
result :
# $Raw_data
# X1 X2 X3 X4 X5
# 1 3.2065101 -0.2331106 0.6306909 -0.35517021 -2.148703085
# 2 -0.4406006 -1.5307214 1.0642876 0.08821547 -0.006447875
# 3 -0.4372114 0.6441982 0.4472678 -0.75549948 0.993803546
# 4 -0.0399572 1.0041989 1.9846562 0.59763520 -0.351116026
# 5 0.1363504 1.4931482 -0.9035270 -0.61957924 2.240344761
# $Noise_matrix
# [,1] [,2] [,3] [,4] [,5]
# [1,] 0.5215023 1.6726942 1.2906344 0.9334373 1.4485531
# [2,] 0.8820923 0.5529964 0.6026034 0.5573415 0.3227387
# [3,] 0.7423318 0.6685330 0.3841618 1.1635156 0.5389766
# [4,] 2.5077895 0.5618750 1.4173889 0.1483538 3.1860982
# [5,] 0.3218608 4.7494683 0.3427328 0.2197831 0.7695381
# $Bias_matrix
# [,1] [,2] [,3] [,4] [,5]
# [1,] 0 0 0 0 0
# [2,] 0 0 0 0 0
# [3,] 0 0 0 0 0
# [4,] 0 0 0 0 0
# [5,] 0 0 0 0 0
# $Final_data
# X1 X2 X3 X4 X5
# 1 3.7280124 1.439584 1.9213253 0.5782671 -0.7001499
# 2 0.4414917 -0.977725 1.6668909 0.6455570 0.3162909
# 3 0.3051204 1.312731 0.8314296 0.4080161 1.5327801
# 4 2.4678323 1.566074 3.4020451 0.7459890 2.8349822
# 5 0.4582112 6.242617 -0.5607942 -0.3997961 3.0098829
The users can choose the type of bias they want to add to their simulated data.
They can either provide their own bias (a (n, p) dimensional matrix) or
choose from the given bias functions. If they choose the given bias function,
they have to provide arguments for the chosen one. We provide bias function
named constant_batch_effect.
n and p denotes the number of samples and features respectively.
b denotes the batch each sample belongs to. Suppose, the samples come from 3
different places. The users can define which sample belongs to which place. If
b = c(1,2,1,2,3,3,2), that means sample1 belongs to batch 1, sample 2 belongs
to batch 2, sample 3 belongs to batch 1, sample 5 belongs to batch 3 and so on.
f denotes the number of features to be affected. If the user chooses f = 4,
then 4 features will be randomly selected.
s = c(1,2,1) means batch 1, 2 and 3 will be affected by 1, 2 and 1
respectively. s denotes the strength of the batch effect, i.e., how much the
feature values within a batch are changed through the batch effect. Here, sample
2 and 5 belong to batch 1 and other samples belong to batch 2. Samples in batch
1 have their feature values increased by s = 1 whereas samples in batch 2 have
their feature values increased by s = 2. Features 1,3,4 and 5 are affected by
the batch effects.
Here is an example :
simulatr::simulate_dataset( n = 7,
p = 8,
base = data.frame(matrix(0, 7, 8)),
bias_func = constant_batch_effect,
bias_func_args = (list(b = c(1,2,1,2,3,3,2),
f = 4,
s = c(1,2,1))))
# result :
# $Raw_data
# X1 X2 X3 X4 X5 X6 X7 X8
# 1 0 0 0 0 0 0 0 0
# 2 0 0 0 0 0 0 0 0
# 3 0 0 0 0 0 0 0 0
# 4 0 0 0 0 0 0 0 0
# 5 0 0 0 0 0 0 0 0
# 6 0 0 0 0 0 0 0 0
# 7 0 0 0 0 0 0 0 0
# $Noise_matrix
# [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
# [1,] 0 0 0 0 0 0 0 0
# [2,] 0 0 0 0 0 0 0 0
# [3,] 0 0 0 0 0 0 0 0
# [4,] 0 0 0 0 0 0 0 0
# [5,] 0 0 0 0 0 0 0 0
# [6,] 0 0 0 0 0 0 0 0
# [7,] 0 0 0 0 0 0 0 0
# $Bias_arguments
# $Bias_arguments$b
# [1] 1 2 1 2 3 3 2
# $Bias_arguments$f
# [1] 4
# $Bias_arguments$s
# [1] 1 2 1
# $Bias_matrix
# [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
# [1,] 1 0 0 1 1 1 0 0
# [2,] 2 0 0 2 2 2 0 0
# [3,] 1 0 0 1 1 1 0 0
# [4,] 2 0 0 2 2 2 0 0
# [5,] 1 0 0 1 1 1 0 0
# [6,] 1 0 0 1 1 1 0 0
# [7,] 2 0 0 2 2 2 0 0
# $Features_affected
# [1] 4 1 6 5
# $Final_data
# X1 X2 X3 X4 X5 X6 X7 X8
# 1 1 0 0 1 1 1 0 0
# 2 2 0 0 2 2 2 0 0
# 3 1 0 0 1 1 1 0 0
# 4 2 0 0 2 2 2 0 0
# 5 1 0 0 1 1 1 0 0
# 6 1 0 0 1 1 1 0 0
# 7 2 0 0 2 2 2 0 0
The users can call a simplified version of constant_batch_effect. If users
define b = 2, then samples will be randomly assigned to 2 different batches.
simulatr::simulate_dataset( n = 5,
p = 5,
base = data.frame(matrix(0, 5, 5)),
bias_func = constant_batch_effect,
bias_func_args = (list(b = 2, f = 4, s = c(1, 2))))
# result :
# $Raw_data
# X1 X2 X3 X4 X5
# 1 0 0 0 0 0
# 2 0 0 0 0 0
# 3 0 0 0 0 0
# 4 0 0 0 0 0
# 5 0 0 0 0 0
# $Noise_matrix
# [,1] [,2] [,3] [,4] [,5]
# [1,] 0 0 0 0 0
# [2,] 0 0 0 0 0
# [3,] 0 0 0 0 0
# [4,] 0 0 0 0 0
# [5,] 0 0 0 0 0
# $Bias_arguments
# $Bias_arguments$b
# [1] 1 1 2 2 2
# $Bias_arguments$f
# [1] 4
# $Bias_arguments$s
# [1] 1 2
# $Bias_matrix
# [,1] [,2] [,3] [,4] [,5]
# [1,] 0 1 1 1 1
# [2,] 0 1 1 1 1
# [3,] 0 2 2 2 2
# [4,] 0 2 2 2 2
# [5,] 0 2 2 2 2
# $Features_affected
# [1] 4 3 2 5
# $Final_data
# X1 X2 X3 X4 X5
# 1 0 1 1 1 1
# 2 0 1 1 1 1
# 3 0 2 2 2 2
# 4 0 2 2 2 2
# 5 0 2 2 2 2
Here, sample 1 and sample 2 belongs to batch 1 and other samples belong to batch 2. Batch 1 is increased by 1 wheras batch 2 is increased by 2.Four featues, feature 2, feature 3, feature 4 and feature 5, are randomly selected for the effect.
In a more simplified version, if the first batch is affected by 0, then user can skip that.
simulatr::simulate_dataset(n = 5,
p = 5,
base = data.frame(matrix(0, 5, 5)),
bias_func = constant_batch_effect,
bias_func_args = (list(b = 2, f = 2, s = 1)))
# result :
# $Raw_data
# X1 X2 X3 X4 X5
# 1 0 0 0 0 0
# 2 0 0 0 0 0
# 3 0 0 0 0 0
# 4 0 0 0 0 0
# 5 0 0 0 0 0
# $Noise_matrix
# [,1] [,2] [,3] [,4] [,5]
# [1,] 0 0 0 0 0
# [2,] 0 0 0 0 0
# [3,] 0 0 0 0 0
# [4,] 0 0 0 0 0
# [5,] 0 0 0 0 0
# $Bias_arguments
# $Bias_arguments$b
# [1] 2 1 1 1 1
# $Bias_arguments$f
# [1] 2
# $Bias_arguments$s
# [1] 0 1
# $Bias_matrix
# [,1] [,2] [,3] [,4] [,5]
# [1,] 0 1 0 1 0
# [2,] 0 0 0 0 0
# [3,] 0 0 0 0 0
# [4,] 0 0 0 0 0
# [5,] 0 0 0 0 0
# $Features_affected
# [1] 4 2
# $Final_data
# X1 X2 X3 X4 X5
# 1 0 1 0 1 0
# 2 0 0 0 0 0
# 3 0 0 0 0 0
# 4 0 0 0 0 0
# 5 0 0 0 0 0Here, feature 2 and 4 are affected. Sample 1 belongs to batch 2. Other samples belong to batch 1. Batch 1 is increased by 0 and batch 2 is increased by 1.
simulatr::simulate_dataset( n = 5,
p = 5,
base = simulate_gse(5, 5, gse = "GSE461"),
bias_func = constant_batch_effect,
bias_func_args = (list(b = 2, f = 4, s = c(1, 2))))
# Result:
# $Raw_data
# GSM7495 GSM7491 GSM7490 GSM7492 GSM7494
# 8207_at 27.3 7.0 243.9 3945.1 11.8
# 8293_at 69.7 58.6 4.2 165.4 6.1
# 3025_s_at 2696.5 11.1 15.6 257.3 15.0
# 2556_at 23.4 738.0 3.0 4.6 53.4
# 10137_at 10.5 39.3 280.6 60.9 250.0
# $Noise_matrix
# [,1] [,2] [,3] [,4] [,5]
# [1,] 0 0 0 0 0
# [2,] 0 0 0 0 0
# [3,] 0 0 0 0 0
# [4,] 0 0 0 0 0
# [5,] 0 0 0 0 0
# $Bias_arguments
# $Bias_arguments$b
# [1] 2 2 2 1 1
# $Bias_arguments$f
# [1] 4
# $Bias_arguments$s
# [1] 1 2
# $Bias_matrix
# [,1] [,2] [,3] [,4] [,5]
# [1,] 2 2 0 2 2
# [2,] 2 2 0 2 2
# [3,] 2 2 0 2 2
# [4,] 1 1 0 1 1
# [5,] 1 1 0 1 1
# $Features_affected
# [1] 2 4 5 1
# $Final_data
# GSM7495 GSM7491 GSM7490 GSM7492 GSM7494
# 8207_at 29.3 9.0 243.9 3947.1 13.8
# 8293_at 71.7 60.6 4.2 167.4 8.1
# 3025_s_at 2698.5 13.1 15.6 259.3 17.0
# 2556_at 24.4 739.0 3.0 5.6 54.4
# 10137_at 11.5 40.3 280.6 61.9 251.0
simulatr::simulate_dataset( n = 20,
p = 4,
base = get_dataset(gse = "GSE461"),
bias_func = constant_batch_effect,
bias_func_args = (list(b = 2, f = 4, s = c(1,2))))
# Result:
# $Raw_data
# GSM7494 GSM7492 GSM7491 GSM7490
# 5141_at 5082.8 5417.0 6886.8 5634.4
# 7689_at 130.3 406.9 423.9 309.4
# 11223_at 60.2 100.6 91.8 64.3
# 8922_at 406.1 593.3 748.8 709.5
# 6530_at 43.1 70.0 57.5 50.5
# 3490_f_at 1.5 1.5 0.3 0.4
# 4225_at 100.0 253.6 269.8 203.1
# 7545_at 504.0 211.2 193.1 204.4
# 2299_at 2.1 16.4 0.9 2.1
# 7578_at 82.4 87.4 85.8 58.6
# 4623_at 732.8 797.7 799.6 1157.6
# 2407_at 31.0 40.5 45.2 52.1
# 2917_s_at 4.4 1.7 1.2 0.7
# 5694_at 929.5 353.1 399.2 387.4
# 9308_at 569.5 468.3 493.5 443.0
# 2701_g_at 1.6 22.5 13.9 11.7
# 6527_at 67.5 36.8 101.5 56.4
# 10824_at 8.9 31.5 60.4 2.8
# 7287_at 13.6 1.1 14.6 18.0
# 4453_at 1048.7 824.4 880.3 851.1
# $Noise_matrix
# [,1] [,2] [,3] [,4]
# [1,] 0 0 0 0
# [2,] 0 0 0 0
# [3,] 0 0 0 0
# [4,] 0 0 0 0
# [5,] 0 0 0 0
# [6,] 0 0 0 0
# [7,] 0 0 0 0
# [8,] 0 0 0 0
# [9,] 0 0 0 0
# [10,] 0 0 0 0
# [11,] 0 0 0 0
# [12,] 0 0 0 0
# [13,] 0 0 0 0
# [14,] 0 0 0 0
# [15,] 0 0 0 0
# [16,] 0 0 0 0
# [17,] 0 0 0 0
# [18,] 0 0 0 0
# [19,] 0 0 0 0
# [20,] 0 0 0 0
# $Bias_arguments
# $Bias_arguments$b
# [1] 1 1 2 1 1 2 2 1 2 2 2 1 1 1 2 2 1 2 2 2
# $Bias_arguments$f
# [1] 4
# $Bias_arguments$s
# [1] 1 2
# $Bias_matrix
# [,1] [,2] [,3] [,4]
# [1,] 1 1 1 1
# [2,] 1 1 1 1
# [3,] 2 2 2 2
# [4,] 1 1 1 1
# [5,] 1 1 1 1
# [6,] 2 2 2 2
# [7,] 2 2 2 2
# [8,] 1 1 1 1
# [9,] 2 2 2 2
# [10,] 2 2 2 2
# [11,] 2 2 2 2
# [12,] 1 1 1 1
# [13,] 1 1 1 1
# [14,] 1 1 1 1
# [15,] 2 2 2 2
# [16,] 2 2 2 2
# [17,] 1 1 1 1
# [18,] 2 2 2 2
# [19,] 2 2 2 2
# [20,] 2 2 2 2
# $Features_affected
# [1] 4 2 3 1
# $Final_data
# GSM7494 GSM7492 GSM7491 GSM7490
# 5141_at 5083.8 5418.0 6887.8 5635.4
# 7689_at 131.3 407.9 424.9 310.4
# 11223_at 62.2 102.6 93.8 66.3
# 8922_at 407.1 594.3 749.8 710.5
# 6530_at 44.1 71.0 58.5 51.5
# 3490_f_at 3.5 3.5 2.3 2.4
# 4225_at 102.0 255.6 271.8 205.1
# 7545_at 505.0 212.2 194.1 205.4
# 2299_at 4.1 18.4 2.9 4.1
# 7578_at 84.4 89.4 87.8 60.6
# 4623_at 734.8 799.7 801.6 1159.6
# 2407_at 32.0 41.5 46.2 53.1
# 2917_s_at 5.4 2.7 2.2 1.7
# 5694_at 930.5 354.1 400.2 388.4
# 9308_at 571.5 470.3 495.5 445.0
# 2701_g_at 3.6 24.5 15.9 13.7
# 6527_at 68.5 37.8 102.5 57.4
# 10824_at 10.9 33.5 62.4 4.8
# 7287_at 15.6 3.1 16.6 20.0
# 4453_at 1050.7 826.4 882.3 853.1simulatr::simulate_dataset( n = 10,
p = 4,
base = get_dataset(gse = "GSE461"),
noise_func = uniform_noise,
noise_func_args = list(min = 1, max = 2),
bias_func = constant_batch_effect,
bias_func_args = list(b = 2, f = 4, s = c(1, 2)))
# Result :
# $Raw_data
# GSM7491 GSM7496 GSM7490 GSM7493
# 4074_at 1056.4 2843.4 1245.3 2154.8
# 6770_i_at 35.4 76.0 40.9 56.2
# 2429_at 18.5 3.6 0.9 8.6
# 6699_at 160.6 100.4 175.4 109.5
# 7968_at 74.7 79.2 38.6 47.4
# 6252_at 10.8 0.3 0.9 0.7
# 8457_at 205.0 161.1 143.7 110.8
# 10683_at 67.2 58.2 74.8 69.9
# 8966_at 1749.2 550.7 950.9 461.6
# 5457_at 19.2 10.0 9.9 12.7
# $Noise_matrix
# [,1] [,2] [,3] [,4]
# [1,] 1.522539 1.901949 1.548870 1.656620
# [2,] 1.938405 1.542918 1.228166 1.194903
# [3,] 1.570219 1.756231 1.451785 1.755073
# [4,] 1.333608 1.053543 1.935255 1.254156
# [5,] 1.504847 1.937689 1.619417 1.198369
# [6,] 1.644201 1.900440 1.313804 1.614920
# [7,] 1.609227 1.218666 1.731578 1.509764
# [8,] 1.374577 1.677683 1.062348 1.729263
# [9,] 1.014870 1.190122 1.528480 1.356725
# [10,] 1.137060 1.782335 1.922753 1.919021
# $Bias_arguments
# $Bias_arguments$b
# [1] 1 2 1 1 2 1 2 1 1 1
# $Bias_arguments$f
# [1] 4
# $Bias_arguments$s
# [1] 1 2
# $Bias_matrix
# [,1] [,2] [,3] [,4]
# [1,] 1 1 1 1
# [2,] 2 2 2 2
# [3,] 1 1 1 1
# [4,] 1 1 1 1
# [5,] 2 2 2 2
# [6,] 1 1 1 1
# [7,] 2 2 2 2
# [8,] 1 1 1 1
# [9,] 1 1 1 1
# [10,] 1 1 1 1
# $Features_affected
# [1] 2 1 3 4
# $Final_data
# GSM7491 GSM7496 GSM7490 GSM7493
# 4074_at 1058.92254 2846.301949 1247.848870 2157.45662
# 6770_i_at 39.33840 79.542918 44.128166 59.39490
# 2429_at 21.07022 6.356231 3.351785 11.35507
# 6699_at 162.93361 102.453543 178.335255 111.75416
# 7968_at 78.20485 83.137689 42.219417 50.59837
# 6252_at 13.44420 3.200440 3.213804 3.31492
# 8457_at 208.60923 164.318666 147.431578 114.30976
# 10683_at 69.57458 60.877683 76.862348 72.62926
# 8966_at 1751.21487 552.890122 953.428480 463.95672
# 5457_at 21.33706 12.782335 12.822753 15.61902simulatr::simulate_dataset( n = 8,
p = 4,
base = simulate_gse(15, 15, "GSE803"),
noise_func = uniform_noise,
noise_func_args = list(min = 1, max = 2),
bias_func = constant_batch_effect,
bias_func_args = list(b = 2, f = 4, s = c(1, 2)))
# Result:
# $Raw_data
# GSM12688 GSM12654 GSM12713 GSM12733
# 1535_at 148.6 101.8 97.0 62.2
# 34373_at 39.7 1077.1 141.0 26.7
# 35203_at 27.7 314.2 533.1 75.4
# 41605_at 458.4 14.6 23.9 2195.2
# 39982_r_at 16.3 3.6 48.6 12.8
# 40126_at 164.1 2.4 9.0 226.4
# 593_s_at 0.9 333.1 2935.4 67.2
# 37360_at 8.2 71.1 178.8 5.4
# $Noise_matrix
# [,1] [,2] [,3] [,4]
# [1,] 1.180408 1.047588 1.495384 1.380375
# [2,] 1.678990 1.515200 1.524956 1.400341
# [3,] 1.382764 1.362757 1.499169 1.422813
# [4,] 1.021458 1.766467 1.304031 1.707219
# [5,] 1.708883 1.326419 1.201463 1.118473
# [6,] 1.406368 1.381837 1.985364 1.383387
# [7,] 1.227164 1.538599 1.979325 1.590795
# [8,] 1.780569 1.495484 1.055557 1.602012
# $Bias_arguments
# $Bias_arguments$b
# [1] 2 2 1 2 1 1 1 2
# $Bias_arguments$f
# [1] 4
# $Bias_arguments$s
# [1] 1 2
# $Bias_matrix
# [,1] [,2] [,3] [,4]
# [1,] 2 2 2 2
# [2,] 2 2 2 2
# [3,] 1 1 1 1
# [4,] 2 2 2 2
# [5,] 1 1 1 1
# [6,] 1 1 1 1
# [7,] 1 1 1 1
# [8,] 2 2 2 2
# $Features_affected
# [1] 2 3 1 4
# $Final_data
# GSM12688 GSM12654 GSM12713 GSM12733
# 1535_at 151.780408 104.847588 100.49538 65.580375
# 34373_at 43.378990 1080.615200 144.52496 30.100341
# 35203_at 30.082764 316.562757 535.59917 77.822813
# 41605_at 461.421458 18.366467 27.20403 2198.907219
# 39982_r_at 19.008883 5.926419 50.80146 14.918473
# 40126_at 166.506368 4.781837 11.98536 228.783387
# 593_s_at 3.127164 335.638599 2938.37933 69.790795
# 37360_at 11.980569 74.595484 181.85556 9.002012 The users can provide their own noise or bias matrix if they want.
# simulatr::simulate_dataset( n = 4,
# p = 4,
# base = simulate_gse(15, 15, "GSE803"),
# noise_func = matrix(1, 4, 4),
# bias_func = matrix(2, 4, 4))
# # Result :
# $Raw_data
# GSM12738 GSM12733 GSM12698 GSM12688
# 40881_at 143.8 88.0 46.8 1324.0
# 32539_at 418.8 188.6 44.0 202.9
# 37466_at 810.9 1303.3 886.9 97.8
# 36708_at 67.4 616.8 553.6 127.8
# $Noise_matrix
# [,1] [,2] [,3] [,4]
# [1,] 1 1 1 1
# [2,] 1 1 1 1
# [3,] 1 1 1 1
# [4,] 1 1 1 1
# $Bias_matrix
# [,1] [,2] [,3] [,4]
# [1,] 2 2 2 2
# [2,] 2 2 2 2
# [3,] 2 2 2 2
# [4,] 2 2 2 2
# $Final_data
# GSM12738 GSM12733 GSM12698 GSM12688
# 40881_at 146.8 91.0 49.8 1327.0
# 32539_at 421.8 191.6 47.0 205.9
# 37466_at 813.9 1306.3 889.9 100.8
# 36708_at 70.4 619.8 556.6 130.8
Provides list of all the platforms(e.g. GPL97) available in NCBI.
utils::head(simulatr::list_platforms(),3)
# A part of the result that can be retrieved by this function :
# Accession Title
# 1 GPL25897 Illumina HiSeq 4000 (Fagopyrum hailuogouense)
# 2 GPL25881 Qiagen Mouse Inflammatory Response and Autoimmunity PCR Array (PAMM-077Z)
# 3 GPL25892 HiSeq X Ten (Rattus rattus)
# Technology Taxonomy Data.Rows Samples.Count Series.Count
# 1 high-throughput sequencing Fagopyrum hailuogouense 0 6 1
# 2 RT-PCR Mus musculus 96 34 1
# 3 high-throughput sequencing Rattus rattus 0 8 1
# Contact Release.Date
# 1 GEO Dec 05, 2018
# 2 Patricia Silveyra Dec 04, 2018
# 3 GEO Dec 04, 2018
The users can retrieve data for a specific platform (e.g. GPL97)
simulatr::get_gpl_data("GPL96")
# # result :
# GEO Accession Title Technology Organism
# a "GPL96" "[HG-U133A] Affymetrix Human Genome U133A Array" "in situ oligonucleotide" "Homo sapiens"
# Status
# a "Public on Mar 11 2002"
Provides information about all series (e.g. GSE465) related to a specific platform (e.g. GPL95)
simulatr::list_datasets(platform = "GPL95")
# # result :
# Accession Title
# 20365 GSE465 Expression profiling in the muscular dystrophies
# 151738 GSE762 CCFAlmasan_CaP1
# 32434 GSE803 GeneNote-Gene Normal tissue Expression
# 74830 GSE1007 Molecular profiles(HG-U95B,C,D,E) of dystrophin-deficient and normal human skeletal muscle
# 147372 GSE1302 primary trophoblast study
# 20322 GSE2508 Expression profiling in adipocytes of obese humans
# 164705 GSE5949 Comparison between cell lines from 9 different cancer tissue (NCI-60) (U95 platform)
# 16539 GSE51625 Expression data from human abdominal, subcutaneous adipose tissue
# Series.Type Taxonomy Sample.Count
# 20365 Expression profiling by array Homo sapiens 57
# 151738 Expression profiling by array Homo sapiens 25
# 32434 Expression profiling by array Homo sapiens 120
# 74830 Expression profiling by array Homo sapiens 86
# 147372 Expression profiling by array Homo sapiens 75
# 20322 Expression profiling by array Homo sapiens 195
# 164705 Expression profiling by array Homo sapiens 300
# 16539 Expression profiling by array Homo sapiens 120
# Datasets Supplementary.Types
# 20365 GDS214;GDS262;GDS264;GDS265;GDS270 CEL
# 151738 GDS719;GDS720;GDS721;GDS722;GDS723
# 32434 GDS422;GDS423;GDS424;GDS425;GDS426
# 74830 GDS609;GDS610;GDS611;GDS612 CEL;EXP;RPT
# 147372
# 20322 GDS1495;GDS1496;GDS1497;GDS1498;GDS3601;GDS3602
# 164705 CEL;EXP
# 16539 CEL
# Supplementary.Links PubMed.ID SRA.Accession
# 20365 ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSEnnn/GSE465/suppl 11121445
# 151738
# 32434 15388519
# 74830 ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE1nnn/GSE1007/suppl 12698323
# 147372 15161964
# 20322 16059715;18424589
# 164705 ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE5nnn/GSE5949/suppl 20053763;26048278;25003721
# 16539 ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE51nnn/GSE51625/suppl 24103848
# Contact Release.Date
# 20365 Eric P Hoffman Jul 16, 2003
# 151738 John Gilmary Hissong Jun 01, 2004
# 32434 Orit Shmueli Nov 19, 2003
# 74830 Judith Haslett Feb 04, 2004
# 147372 Brig Mecham Apr 13, 2004
# 20322 Yong-Ho Lee Jan 01, 2006
# 164705 Uma T Shankavaram Aug 06, 2007
# 16539 Carol Shoulders Oct 29, 2013- Create a new feature branch
- Commit your changes
- Push your changes
- Create a pull request
- Wait until all tests have completed
- Merge the pull request
To publish a version to CRAN, run the following commands in an active R session:
devtools::document() # Update documentation
rcmdcheck::rcmdcheck( # Run `R CMD check` for this package
args=c("--no-manual", "--as-cran"),
build_args=c("--no-manual"),
check_dir="check"
)
devtools::revdep() # Run `R CMD check` for all dependencies
devtools::spell_check() # Check spelling of package
devtools::release() # Builds, tests and submits the package to CRAN.
# Manual submission can be done at: https://cran.r-project.org/submit.htmlSource: https://r-pkgs.org/release.html
| MOSim | MadSim | Simulatr | ||
|---|---|---|---|---|
| number of features can be specified | x | x | x | |
| percentage of differentially expressed genes can be specified | x | x | x | |
| correlation structure can be specified | x | x | ||
| type of data (RNAseq/DNAseq) can be specified | x | x | ||
| platform (HGU133a, ...) can be specified | x | |||
| standard deviation or noise can be specified | x | x | ||
| ability to work with base dataset | x | x | x | |
| upper and lower limit can be specified | x | x | ||
| easy to read instruction | x |
- x means yes
- Omics Simla https://omicssimla.sourceforge.io/
- micro array data simulation https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5003477/
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