## ----echo = FALSE, message = FALSE, warning = FALSE--------------------------- library(BiocStyle) ## ----load-libs, message = FALSE, warning = FALSE----------------------------- library(dStruct) library(tidyverse) ## ----------------------------------------------------------------------------- data(lai2019) ## ----------------------------------------------------------------------------- ls() ## ----------------------------------------------------------------------------- class(lai2019) ## ----------------------------------------------------------------------------- names(lai2019) %>% head() ## ----------------------------------------------------------------------------- class(lai2019[[1]]) ## ----------------------------------------------------------------------------- head(lai2019[["YAL042W"]], n= 20) ## ----warning=FALSE------------------------------------------------------------ dStruct(rdf = lai2019[["YAL042W"]], reps_A = 3, reps_B = 2, batches = TRUE, min_length = 21, between_combs = data.frame(c("A3", "B1", "B2")), within_combs = data.frame(c("A1", "A2", "A3")), ind_regions = TRUE) ## ----warning=FALSE------------------------------------------------------------ res <- dStructome(lai2019, 3, 2, batches= TRUE, min_length = 21, between_combs = data.frame(c("A3", "B1", "B2")), within_combs = data.frame(c("A1", "A2", "A3")), ind_regions = TRUE, processes = 1) ## ----------------------------------------------------------------------------- head(res) ## ----------------------------------------------------------------------------- data(wan2014) ## ----------------------------------------------------------------------------- ls() ## ----------------------------------------------------------------------------- wan2014[[1]] ## ----------------------------------------------------------------------------- names(wan2014) %>% head() ## ----------------------------------------------------------------------------- dStructGuided(wan2014[[1]], reps_A = 2, reps_B = 1) ## ----warning=FALSE------------------------------------------------------------ res_predefined_regs <- dStructome(wan2014, reps_A = 2, reps_B = 1, method = "guided", processes = 1) ## ----------------------------------------------------------------------------- head(res_predefined_regs) ## ----------------------------------------------------------------------------- toPlot <- res@elementMetadata %>% data.frame() %$% magrittr::extract(t, order(FDR)) %>% head(., n = 1) toPlot ## ----message=FALSE, warning=FALSE--------------------------------------------- plotDStructurome(rl = lai2019[toPlot], diff_regions = subset(res, t == toPlot), outfile = paste0("DRRs_in_", toPlot), fdr = 0.05, ylim = c(-0.05, 3)) ## ----------------------------------------------------------------------------- sessionInfo()