DEPRECATED: Read in cell-specific bam files for SMART-seq2 measurement This function is deprecated. Please use velocyto.py to prepare loom file from SMART-seq2 bam files.
read.smartseq2.bams(bam.files, annotation.file, min.exon.count = 100,
n.cores = defaultNCores())list of bam files
refFlat genome annotation file (use gtfToGenePred to generate refFlat file from gtf)
minimum number of reads (across all cells) for an exon to be considered expressed in the dataset
number of cores to use
a list containing: emat - exonic (spliced) read count matrix ; iomat - intronic (unspliced) matrix; smat - spanning read matrix; base.df - data frame containing gene structural information; exons - exon annotation and read counts; genes - gene annotation table with additional structural info; expr.lstat - gene length statistics when considering only expressed exons