## ----setup, include = FALSE--------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ---- message=FALSE----------------------------------------------------------- # The dataset package library(TENxBUSData) library(BUSpaRse) library(Matrix) library(zeallot) library(ggplot2) ## ----------------------------------------------------------------------------- TENxBUSData(".", dataset = "hgmm100") ## ----------------------------------------------------------------------------- tr2g <- transcript2gene(species = c("Homo sapiens", "Mus musculus"), type = "vertebrate", kallisto_out_path = "./out_hgmm100", ensembl_version = 99, write_tr2g = FALSE) ## ----------------------------------------------------------------------------- head(tr2g) ## ----------------------------------------------------------------------------- c(gene_count, tcc) %<-% make_sparse_matrix("./out_hgmm100/output.sorted.txt", tr2g = tr2g, est_ncells = 1e5, est_ngenes = nrow(tr2g)) ## ----------------------------------------------------------------------------- dim(gene_count) ## ----------------------------------------------------------------------------- tot_counts <- Matrix::colSums(gene_count) summary(tot_counts) ## ----------------------------------------------------------------------------- df1 <- get_knee_df(gene_count) infl1 <- get_inflection(df1) ## ----------------------------------------------------------------------------- knee_plot(df1, infl1) ## ----------------------------------------------------------------------------- gene_count <- gene_count[, tot_counts > infl1] dim(gene_count) ## ----------------------------------------------------------------------------- dim(tcc) ## ----------------------------------------------------------------------------- tot_counts <- Matrix::colSums(tcc) summary(tot_counts) ## ----------------------------------------------------------------------------- df2 <- get_knee_df(tcc) infl2 <- get_inflection(df2) ## ----------------------------------------------------------------------------- knee_plot(df2, infl2) ## ----------------------------------------------------------------------------- tcc <- tcc[, tot_counts > infl2] dim(tcc) ## ----------------------------------------------------------------------------- sessionInfo()