import_droplet_txis: import droplet RNAseq data (usually from Alevin) into a...

In trichelab/velocessor: The world's dumbest single-cell RNA velocity calculator and loader

Description

This function is usually called by process_velo_txis(). quants is, like in import_plate_txis, a bunch of directories with quantifications in them. QC does not exist in import_plate_txis, but it is a flag to perform rudimentary quality control for droplet data (and is enabled by default). sep is the separator character between the assigned sample name and the trimmed barcode.

Usage

import_droplet_txis(
  quants,
  feats = NULL,
  type = c("alevin"),
  QC = TRUE,
  tpms = FALSE,
  su_tpms = FALSE,
  sep = "_",
  fixrn = TRUE,
  ...
)

Arguments

quants	Directories containing droplet quantification results
feats	optional file with intron-exon-gene mappings (guess)
type	What type of quantifications are these? ("alevin")
QC	Perform rudimentary quality control? (TRUE)
tpms	compute TPMs? (FALSE; can create a CHOLMOD error)
su_tpms	compute spliced/unspliced TPMs? (FALSE; as above)
sep	What string separates sample name from barcode? ("_")
fixrn	Fix goofy versioned ENSEMBL gene names? (TRUE)
...	additional parameters to pass to tximport, if any

Details

FIXME: Add Kallisto support and Arkas style txome/repeatome/spikeome support.

TPM calculation is disabled by default due to a tendency to crash sessions. The function velocessor::add_tpm handles the grunt work for this at present. It would probably be a good idea to do it more efficiently (e.g. in C++).

Value

     A SingleCellExperiment with 'spliced' & 'unspliced' assays.

trichelab/velocessor documentation built on Jan. 5, 2022, 6:27 p.m.