read.smartseq2.bams: read.smartseq2.bams
In velocyto-team/velocyto.R: RNA velocity estimation in R
Description
Usage
Arguments
Value
View source: R/momentum_routines.R
Description
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.
Usage
1
2
read.smartseq2.bams(bam.files, annotation.file, min.exon.count = 100,
n.cores = defaultNCores())
Arguments
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
Value
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
velocyto-team/velocyto.R documentation built on Dec. 8, 2019, 3:07 a.m.
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Description Usage Arguments Value
View source: R/momentum_routines.R
Description
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.
Usage
1 2 | read.smartseq2.bams(bam.files, annotation.file, min.exon.count = 100,
n.cores = defaultNCores())
|
Arguments
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 |
Value
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
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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