Using cellrangerRkit to read in 10X genomics results in R

read10x.R

#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()