## ---- echo=FALSE-------------------------------------------------------------- library(knitr) opts_chunk$set(cache=FALSE, error=FALSE) ## ----setup, include=FALSE----------------------------------------------------- knitr::opts_chunk$set(echo = TRUE) ## ----install------------------------------------------------------------------ if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("SeqGate") ## ----load_SeqGate------------------------------------------------------------- library(SeqGate) ## ----load_dataTest------------------------------------------------------------ data(data_MiTF_1000genes) head(data_MiTF_1000genes) ## ----define_cond-------------------------------------------------------------- cond<-c("A","A","B","B","A","B") ## ----create_se---------------------------------------------------------------- rowData <- DataFrame(row.names=rownames(data_MiTF_1000genes)) colData <- DataFrame(Conditions=cond) counts_strub <- SummarizedExperiment( assays=list(counts=data_MiTF_1000genes), rowData=rowData, colData=colData) ## ----apply_basic-------------------------------------------------------------- counts_strub <- applySeqGate(counts_strub,"counts","Conditions") ## ----get_kept_features-------------------------------------------------------- keptGenes <- assay(counts_strub[rowData(counts_strub)$onFilter == TRUE,]) head(keptGenes) dim(keptGenes) ## ----threshold---------------------------------------------------------------- metadata(counts_strub)$threshold ## ----get_filtered------------------------------------------------------------- filteredOut <- assay(counts_strub[rowData(counts_strub)$onFilter == FALSE,]) head(filteredOut) ## ----apply_custom------------------------------------------------------------- counts_strub <- applySeqGate(counts_strub,"counts","Conditions", prop0=1/3, percentile=0.8, propUpThresh=0.5) ## ----sessionInfo-------------------------------------------------------------- sessionInfo()