Showing content from https://www.bioconductor.org/packages/release/bioc/html/../vignettes/infercnv/inst/doc/inferCNV.R below:
## ----install, eval=FALSE------------------------------------------------------ # if (!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("infercnv") ## ----install-optionals, eval = FALSE------------------------------------------ # install.packages("tibble") # # install.packages("devtools") # devtools::install_github("bmbroom/tsvio") # devtools::install_github("bmbroom/NGCHMR", ref="stable") # devtools::install_github("broadinstitute/inferCNV_NGCHM") # ## ----setup, include=FALSE----------------------------------------------------- knitr::opts_chunk$set(echo = TRUE) library(infercnv) ## ----------------------------------------------------------------------------- infercnv_obj = CreateInfercnvObject( raw_counts_matrix="../inst/extdata/oligodendroglioma_expression_downsampled.counts.matrix.gz", annotations_file="../inst/extdata/oligodendroglioma_annotations_downsampled.txt", delim="\t", gene_order_file="../inst/extdata/gencode_downsampled.EXAMPLE_ONLY_DONT_REUSE.txt", ref_group_names=c("Microglia/Macrophage","Oligodendrocytes (non-malignant)")) ## ----results="hide"----------------------------------------------------------- out_dir = tempfile() infercnv_obj_default = infercnv::run( infercnv_obj, cutoff=1, # cutoff=1 works well for Smart-seq2, and cutoff=0.1 works well for 10x Genomics out_dir=out_dir, cluster_by_groups=TRUE, plot_steps=FALSE, denoise=TRUE, HMM=FALSE, no_prelim_plot=TRUE, png_res=60 ) ## ----echo=FALSE--------------------------------------------------------------- knitr::include_graphics(paste(out_dir, "infercnv.png", sep="/")) ## ----sessioninfo, echo=FALSE, tidy=TRUE, tidy.opts=list(width.cutoff=60), out.width=60---- sessionInfo()
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