create_tt_from_cellRanger_sc: Create tt object from cellRanger results

In stemangiola/ttSc: Friendly tidy wrappers for facilitating transcriptional analyses

Create tt object from cellRanger results

Description

Create tt object from cellRanger results

Usage

create_tt_from_cellRanger_sc(
  dir_names,
  min.transcripts = 400,
  min.cells = 5,
  high.mito.thresh = 0.08,
  high.umi.thresh = 10000,
  species,
  genome = switch(tolower(species), human = "hg38", mouse = "mm10",
    stop("tidysc says: species not present"))
)

Arguments

dir_names	A character array with the output directories of cellRanger if run from internal function
min.transcripts	An integer with the threshold of the minimum number of genes allowed for each cell
min.cells	An integer with the threshold of the minimum anumber of cells allowed for each sample
high.mito.thresh	An numeric with the threshold of the maximum fraction of reads from mitochondrion. Used for filtering
high.umi.thresh	An numeric with the threshold of the maximum fraction of umis. Used for filtering
species	A character name of the species
genome	A character name of the mapping genome used

Value

A tt object

stemangiola/ttSc documentation built on Dec. 8, 2022, 2:37 a.m.