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.Rbuildignore (28, 2020-12-14)
DESCRIPTION (831, 2020-12-14)
NAMESPACE (1039, 2020-12-14)
R (0, 2020-12-14)
R\design_data.R (17602, 2020-12-14)
R\get_mix_parameters.R (3194, 2020-12-14)
R\simulate.R (10700, 2020-12-14)
R\supp_de.R (8864, 2020-12-14)
R\supp_simulate.R (5177, 2020-12-14)
inst (0, 2020-12-14)
inst\docs (0, 2020-12-14)
inst\docs\joint-manual (0, 2020-12-14)
inst\docs\joint-manual\design_summary.pdf (11971, 2020-12-14)
inst\docs\joint-manual\design_summary.txt (1062, 2020-12-14)
inst\docs\scDesign.pdf (84937, 2020-12-14)
inst\docs\sep-manual (0, 2020-12-14)
inst\docs\sep-manual\design_summary.pdf (12286, 2020-12-14)
inst\docs\sep-manual\design_summary.txt (1381, 2020-12-14)
inst\extdata (0, 2020-12-14)
inst\extdata\astrocytes.rds (635221, 2020-12-14)
inst\extdata\oligodendrocytes.rds (403112, 2020-12-14)
man (0, 2020-12-14)
man\design_data.Rd (2611, 2020-12-14)
man\design_joint.Rd (2745, 2020-12-14)
man\design_sep.Rd (2853, 2020-12-14)
scDesign.Rproj (386, 2020-12-14)
vignettes (0, 2020-12-14)
vignettes\scDesign-vignette.Rmd (6118, 2020-12-14)
vignettes\scDesign-vignette.html (794400, 2020-12-14)
vignettes\scDesign-vignette.pdf (159957, 2020-12-14)
vignettes\scdesign.R (2647, 2020-12-14)

scDesign: a statistical simulator for rational scRNA-seq experimental design ================ Wei Vivian Li 2020-12-13 ## Latest News > 2020/12/13: Version 1.1.0 released! > 2019/03/18: Version 1.0.0 released! ## Introduction Any suggestions on the package are welcome! For technical problems, please report to [Issues](https://github.com/Vivianstats/scDesign/issues). For suggestions and comments on the method, please contact Dr. Vivian Li () or Dr. Jessica Li (). ## Installation The package is not on CRAN yet. For installation please use the following codes in `R` ``` r install.packages("devtools") library(devtools) install_github("Vivianstats/scDesign") ``` ## Quick start `scDesign` has three main functions: - `design_data` for simulation of scRNA-seq data - `design_sep` for scRNA-seq experimental design assuming two cell states are sequenced independetly - `design_joint` for scRNA-seq experimental design assuming two cell states are sequenced together For detailed usage, please refer to the package [manual](https://github.com/Vivianstats/scDesign/blob/master/inst/docs/) or [vignette](https://github.com/Vivianstats/scDesign/blob/master/vignettes/scDesign-vignette.Rmd). ### `design_data` `design_data` simulates additional scRNA-seq data by estimating gene expression parameters from a real scRNA-seq dataset. When `ngroup = 1`, it each time simulates a single dataset based on user-specified total read number `S` and cell number `ncell`. ``` r realcount1 = readRDS(system.file("extdata", "astrocytes.rds", package = "scDesign")) simcount1 = design_data(realcount = realcount1, S = 1e7, ncell = 1000, ngroup = 1, ncores = 1) realcount1[1:3, 1:3] #> GSM1657885 GSM1657932 GSM1657938 #> 1/2-SBSRNA4 0 0 0 #> A2M 0 0 34 #> A2ML1 0 0 25 simcount1[1:3, 1:3] #> cell1 cell2 cell3 #> gene1 0 0 0 #> gene2 0 0 68 #> gene3 0 0 1 ``` When `ngroup > 1`, it simulates `ngroup` datasets following a specified differentiation path. ``` r simdata = design_data(realcount = realcount1, S = rep(1e7,3), ncell = rep(100,3), ngroup = 3, pUp = 0.03, pDown = 0.03, fU = 3, fL = 1.5, ncores = 1) # simdata is a list of three elements names(simdata) #> [1] "count" "genesUp" "genesDown" # count matrix of the cell state 2 simdata$count[[2]][1:3, 1:3] #> C2_1 C2_2 C2_3 #> gene1 132 0 0 #> gene2 6 2 6 #> gene3 0 0 0 # up-regulated genes from state 1 to state 2 simdata$genesUp[[2]][1:3] #> [1] "gene1655" "gene614" "gene6057" # down-regulated genes from state 1 to state 2 simdata$genesDown[[2]][1:3] #> [1] "gene1958" "gene4631" "gene4888" ``` ### `design_sep` `design_sep` assists experimental design by selecting the optimal cell numbers for the two cell states in scRNA-seq, so that the subsequent DE analysis becomes most accurate based on the user-specified criterion. It assumes that cells from the two states are prepared as two separate libraries and sequenced independently. ``` r realcount1 = readRDS(system.file("extdata", "astrocytes.rds", package = "scDesign")) realcount2 = readRDS(system.file("extdata", "oligodendrocytes.rds", package = "scDesign")) # candidate cell numbers for experimental design ncell = cbind(2^seq(6,11,1), 2^seq(6,11,1)) prlist = design_sep(realcount1, realcount2, ncell = ncell, de_method = "ttest", ncores = 10) # returns a list of five elements names(prlist) #> precision recall TN F1 F2 prlist$precision #> p_thre ***vs*** 128vs128 256vs256 512vs512 1024vs1024 2048vs2048 #> 0.01 0.332 0.272 0.178 0.121 0.084 0.056 #> 0.001 0.448 0.361 0.231 0.147 0.097 0.063 #> 1e-04 0.532 0.434 0.282 0.175 0.11 0.07 #> 1e-05 0.599 0.491 0.331 0.203 0.124 0.076 #> 1e-06 0.***9 0.534 0.375 0.231 0.138 0.083 ``` `design_sep` also saves the analysis results to a [txt file](https://github.com/Vivianstats/scDesign/blob/master/inst/docs/sep-manual/design_summary.txt) and a set of power analysis [plots](https://github.com/Vivianstats/scDesign/blob/master/inst/docs/sep-manual/design_summary.pdf). ### `design_joint` `design_joint` assists experimental design by selecting the optimal (total) cell number for a cell population that contains the two cell states of interest, so that the subsequent DE analysis becomes most accurate based on the user-specified criterion. It assumes that cells from the two states are prepared in the same library and sequenced together. ``` r # candidate cell numbers for experimental design ncell = round(2^seq(9,13,1)) prlist = design_joint(realcount1, realcount2, prop1 = 0.2, prop2 = 0.15, ncell = ncell, de_method = "ttest", ncores = 10) # returns a list of five elements names(prlist) #> precision recall TN F1 F2 prlist$recall #> 512 1024 2048 4096 8192 #> 0.01 0.315 0.33 0.259 0.176 0.111 #> 0.001 0.235 0.281 0.24 0.169 0.108 #> 1e-04 0.176 0.236 0.22 0.162 0.105 #> 1e-05 0.133 0.1*** 0.2 0.155 0.102 #> 1e-06 0.103 0.166 0.181 0.147 0.099 ``` `design_joint` also saves the analysis results to a [txt file](https://github.com/Vivianstats/scDesign/blob/master/inst/docs/joint-manual/design_summary.txt) and a set of power analysis [plots](https://github.com/Vivianstats/scDesign/blob/master/inst/docs/joint-manual/design_summary.pdf). ## Citation Li, Wei Vivian, and Jingyi Jessica Li. "A statistical simulator scDesign for rational scRNA-seq experimental design." Bioinformatics 35, no. 14 (2019): i41-i50. [Link](https://doi.org/10.1093/bioinformatics/btz321)

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