Created
May 5, 2017 20:44
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Using cellrangerRkit to read in 10X genomics results in R
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| #credit to @myajima | |
| library(cellrangerRkit) #install using https://s3-us-west-2.amazonaws.com/10x.files/supp/cell-exp/rkit-install-1.1.0.R | |
| pipestance_path <-getwd() | |
| download_sample(sample_name="pbmc3k", | |
| sample_dir=pipestance_path, | |
| host="https://s3-us-west-2.amazonaws.com/10x.files/samples/cell/") | |
| gbm <- load_cellranger_matrix(pipestance_path) | |
| analysis_results <-load_cellranger_analysis_results(pipestance_path) | |
| use_genes <- get_nonzero_genes(gbm) | |
| gbm_bcnorm <- normalize_barcode_sums_to_median(gbm[use_genes,]) | |
| gbm_log <- log_gene_bc_matrix(gbm_bcnorm,base=10) | |
| use_genes <- which(rowSums(exprs(gbm_log)>0)>100) | |
| cmatp<-exprs(gbm_bcnorm)[use_genes,] | |
| library(pheatmap) | |
| pdf("heatmap.pdf") | |
| pheatmap(log(cmatp)) | |
| dev.off() |
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