load_STARsolo_data: Make monocle3 cell_data_set using STARsolo

Description Usage Arguments Value

View source: R/read_tenx.R

Description

This function reads a vector of STARsolo "out" folders for .mtx and .tsv files. This function will create a cds of the data using cellranger thresholds for filtering out droplets that do not contain cells. Optionally, this function can return the unfiltered data as well for further manipulation (ie adjustment of droplet thresholds) if desired.

Usage

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load_STARsolo_data(
  folders,
  samplenames = NULL,
  unfiltered = F,
  empty.droplet.threshold = 15,
  expressed_genes = TRUE,
  count_method = "Gene",
  cell_min = 1
)

Arguments

folders

A vector of STARsolo folders (full folder name is ideal). These must contain an "outs" subfolders with three files: 1) features.tsv, 2) barcodes.tsv, and 3) matrix.mtx.

samplenames

An optional vector that corresponds to the names you would like to give to each element in filelist.

unfiltered

This parameter, if true, returns a list containing 1) the filtered cds, 2) a list of unfiltered cds for each sample in 'folders'.

empty.droplet.threshold

minimum number of umis per droplet to include in unfiltered output (default 15)

expressed_genes

If true, this option removes genes that do not have expression in at least a minumum number of cells (cell_min parameter)

count_method

(required) - A string denoting STARsolo output counting method. (one of either: Gene, GeneFull, SJ, Velocyto)

cell_min

Minimum number of cells that a gene needs to be expressed for the gene to be included in the

Value

a cell_data_set object or a list of items if unfiltered data is returned (see unfiltered)


scfurl/m3addon documentation built on Aug. 9, 2021, 5:30 p.m.