# #——安装,eval = FALSE ------------------------------------------------------ # 如果(!requireNamespace("BiocManager"，悄悄的= TRUE) # install.packages("BiocManager") # BiocManager::install(" intercnv ") ## ----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/ intercnv_ngchm ") ## ----setup，包括= FALSE ----------------------------------------------------- knitr: opts_chunk美元(echo = TRUE)库(infercnv ) ## ----------------------------------------------------------------------------- infercnv_obj = CreateInfercnvObject (raw_counts_matrix = " . . /本月/ extdata / oligodendroglioma_expression_downsampled.counts.matrix.gz”,annotations_file = " . . /本月/ extdata / oligodendroglioma_annotations_downsampled.txt”,delim =“t \”,gene_order_file="../inst/extdata/gencode_downsampled.EXAMPLE_ONLY_DONT_REUSE.txt"， ref_group_names=c("Microglia/巨噬细胞"，"Oligodendrocytes (nonmalignant)")) ## ---- results="hide"---------------------------------------------------------- out_dir= tempfile() intercnv_obj_default = intercnv::run(intercnv_obj, cutoff=1， # cutoff=1适用于Smart-seq2, cutoff=0.1适用于10x Genomics out_dir=out_dir, cluster_by_groups=TRUE, plot_steps=FALSE, noisise =TRUE, HMM=FALSE，no_prelim_plot = TRUE, png_res = 60 ) ## ---- 回声= FALSE -------------------------------------------------------------- knitr:: include_graphics(粘贴(out_dir“infercnv.png”,9月 ="/")) ## ---- sessioninfo,呼应= FALSE,整洁= TRUE, tidy.opts = (width.cutoff = 60)列表,。宽度= 60——sessionInfo ()