TRUE,diagnostics=FALSE,remove_genes_at_chr_ends=FALSE,prune_outliers=FALSE,mask_nonDE_genes=FALSE,mask_nonDE_pval=0.05,test.use="wilcoxon",require_DE_all_normals="any",hspike_aggregate_normals=FALSE,no_plot=FALSE,no_prelim_plot=FALSE,output_format="png",useRaster=TRUE,up_to_step=100) ...
ref_group_names = c("endothelial_normal","fibroblast_normal"), delim ="\t")# Make sure that chrmosomes are ordered correctlyslot(infercnv_obj,"gene_order")[,"chr"] <- factor(slot(infercnv_obj,"gene_order")[,"chr"], levels = c("chr1","chr2","chr3","chr4","chr5","chr6"...
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plot_cnv(infercnv_obj, out_dir='../example_output/', output_filename='infercnv.denoised', x.range="auto", x.center=1, title="denoised", png_res=60, color_safe_pal = FALSE) ``` ```{r, echo=FALSE} knitr::include_graphics("../example_output/infercnv.denoised.png") ``` ...
hspike_aggregate_normals =FALSE, no_plot =FALSE, no_prelim_plot =FALSE, output_format ="png", useRaster =TRUE, up_to_step =100) 多到让人头皮发麻! 其中文献运行infercnv::run的时候,下面两个参数,都是默认值: HMM参数 whensetto True, runs HMM to predict CNV level (default: FALSE) ...
#新建,原来没有这个文件夹>## 文献的代码:#14:58开始>start_time<-Sys.time()>## 文献的代码:#14:58开始>start_time<-Sys.time()>infercnv_obj2=infercnv::run(infercnv_obj,+cutoff=0.1,# cutoff=1 works well for Smart-seq2, and cutoff=0.1 works well for 10x Genomics+out_dir='plot_out/'...
STEP 10: Smoothing data per cell by chromosome INFO [2021-03-11 11:01:20] smooth_by_chromosome: chr: chr1 INFO [2021-03-11 11:01:20] smooth_by_chromosome: chr: chr10 INFO [2021-03-11 11:01:21] smooth_by_chromosome: chr: chr11 INFO [2021-03-11 11:01:21] smooth_by_chromo...
num_threads = 4, plot_steps = FALSE, resume_mode = TRUE, png_res = 300, plot_probabilities = TRUE, save_rds = TRUE, save_final_rds = TRUE, diagnostics = FALSE, remove_genes_at_chr_ends = FALSE, prune_outliers = FALSE, mask_nonDE_genes = FALSE, mask_nonDE_pval = 0.05, test....
TRUE,diagnostics=FALSE,remove_genes_at_chr_ends=FALSE,prune_outliers=FALSE,mask_nonDE_genes=FALSE,mask_nonDE_pval=0.05,test.use="wilcoxon",require_DE_all_normals="any",hspike_aggregate_normals=FALSE,no_plot=FALSE,no_prelim_plot=FALSE,output_format="png",useRaster=TRUE,up_to_step=100)...
+ ref_group_names=c("Microglia/Macrophage","Oligodendrocytes (non-malignant)")) INFO [2020-07-06 12:40:59] Parsing matrix: C:/Users/wlx/Documents/R/win-library/3.6/infercnv/extdata/oligodendroglioma_expression_downsampled.counts.matrix.gz ...