## ----style, echo=FALSE, results='asis'------------------------------------- BiocStyle::markdown() ## ----setup, include=FALSE-------------------------------------------------- knitr::opts_chunk$set(echo = TRUE) options(warn = -1) library(dplyr) library(tibble) library(methods) library(perturbatr) data(rnaiscreen) rnaiscreen <- dataSet(rnaiscreen) %>% dplyr::select(Condition, Replicate, GeneSymbol, Perturbation, Readout, Control, Design, ScreenType, Screen) %>% as.tibble() ## ---- include=TRUE, size="tiny"-------------------------------------------- head(rnaiscreen) ## ---- include=TRUE, eval=TRUE---------------------------------------------- rnaiscreen <- methods::as(rnaiscreen, "PerturbationData") ## ---- eval=TRUE, include=TRUE---------------------------------------------- rnaiscreen dataSet(rnaiscreen) ## ---- eval=TRUE, include=TRUE---------------------------------------------- perturbatr::filter(rnaiscreen, Readout > 0) ## ---- eval=TRUE, include=TRUE---------------------------------------------- perturbatr::filter(rnaiscreen, Readout > 0, Replicate == 2) ## ---- eval=TRUE, include=TRUE---------------------------------------------- dh <- perturbatr::filter(rnaiscreen, Readout > 0, Replicate == 2) rbind(dh, dh) ## ---- eval=TRUE, include=TRUE, fig.align="center", fig.width=4, message=FALSE---- plot(rnaiscreen) ## -------------------------------------------------------------------------- dataSet(rnaiscreen) %>% str() ## -------------------------------------------------------------------------- dataSet(rnaiscreen) %>% pull(ScreenType) %>% unique() ## ---- eval=TRUE, include=TRUE, warning=FALSE, message=FALSE---------------- frm <- Readout ~ Condition + (1|GeneSymbol) + (1|Condition:GeneSymbol) + (1|ScreenType) + (1|Condition:ScreenType) res.hm <- hm(rnaiscreen, formula = frm) ## ---- include=TRUE, fig.align="center", fig.width=4, message=FALSE--------- pl <- plot(res.hm) pl[[1]] ## ----include=TRUE, fig.align="center", fig.width=4, message=FALSE---------- pl[[2]] ## ----include=TRUE, fig.align="center", fig.width=4, message=FALSE---------- graph <- readRDS( system.file("extdata", "graph_small.rds",package = "perturbatr")) diffu <- diffuse(res.hm, graph=graph, r=0.3) ## ----include=TRUE, fig.align="center", fig.width=4, message=FALSE---------- plot(diffu) ## ----eval=TRUE, include=TRUE----------------------------------------------- sessionInfo()