import_kallisto_txis: import plate-seq runs from Kallisto into a...

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

Description

Automated (more or less) importation of STORM-seq and SMART-seq123 data for downstream attempts at merging, index visualization, etc. Assumes that users will quantify against ENSEMBL transcripts instead of ridiculous crap like GENCODE and similar. Default is ERCC spikes, ENSembl transcripts, and if found, intronic quantifications of the same. Everything else gets labeled as 'viruses_and_repeats' since in our transcriptomes, that's what it is. If altExps is set to FALSE, no splitting will be attempted.

Usage

import_kallisto_txis(
  runs,
  what = c(tpm = "tpm", counts = "est_counts", eff_length = "eff_length"),
  altExps = TRUE,
  asgenes = FALSE,
  t2g = NULL,
  BPPARAM = bpparam(),
  ...
)

Arguments

runs	a vector of .tsv file paths (usually abundance.tsv) w/names
what	columns to import (default: tpm, est_counts, eff_length)
altExps	split spliced, unspliced, spikes, viruses & repeats? (TRUE)
asgenes	collapse transcripts to genes? (implies altExps & t2g)
t2g	data.frame with tx2gene mappings (required if asgenes)
BPPARAM	optional BiocParallel parameter object for bplapply()
...	additional parameters to pass to .split_altExps

Value

     A SingleCellExperiment

Examples

t2g <- read.delim("../hs_mm_spikes_repeats_ens100.trimmed.velo.tx2gene.tsv",
                  sep="\t", row.names=1, head=FALSE)
t2g <- t2g[grep("ENS", rownames(t2g)), , drop=FALSE]

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