diff --git a/DESCRIPTION b/DESCRIPTION index b9130e4..8e80ad5 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: mnem Type: Package Title: Mixture Nested Effects Models -Version: 0.99.7 +Version: 0.99.8 Author: Martin Pirkl Maintainer: Martin Pirkl Description: Mixture Nested Effects Models (mnem) is an extension of Nested Effects Models and allows for the analysis of single cell perturbation data provided by methods like Perturb-Seq (Dixit et al., 2016) or Crop-Seq (Datlinger et al., 2017). In those experiments each of many cells is perturbed by a knock-down of a specific gene, i.e. several cells are perturbed by a knock-down of gene A, several by a knock-down of gene B, ... and so forth. The observed read-out has to be multi-trait and in the case of the Perturb-/Crop-Seq gene are expression profiles for each cell. mnem uses a mixture model to simultaneously cluster the cell population into k clusters and and infer k networks causally linking the perturbed genes for each cluster. The mixture components are inferred via an expectation maximization algorithm. diff --git a/R/mnems.r b/R/mnems.r index d095088..f0aed02 100644 --- a/R/mnems.r +++ b/R/mnems.r @@ -798,7 +798,7 @@ plot.bootmnem <- function(x, reduce = TRUE, ...) { adj[bidi] <- (adj2+t(adj2))[bidi] diag(adj) <- 0 dnf <- adj2dnf(apply(adj, c(1,2), ceiling)) - dnf <- dnf[-(1:nrow(adj))] + dnf <- dnf[-seq_len(nrow(adj))] freq <- as.vector(t(adj)) freq <- freq[which(freq != 0)] dnfs <- c(dnfs, dnf)