Description Usage Arguments Value
View source: R/momentum_routines.R
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.
1 2 3 4 5 6 | read.smartseq2.bams(
bam.files,
annotation.file,
min.exon.count = 100,
n.cores = defaultNCores()
)
|
bam.files |
list of bam files |
annotation.file |
refFlat genome annotation file (use gtfToGenePred to generate refFlat file from gtf) |
min.exon.count |
minimum number of reads (across all cells) for an exon to be considered expressed in the dataset |
n.cores |
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
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