remove_outliers: Remove outlier genes and cells.

In juliendelile/Antler: ANother Transcriptome Lineage ExploreR

Description

This method excludes cells with a total read counts outside of a specified interval, cells having less than a certain number of expressed genes, and genes expressed in less than a given number of cells.

Arguments

lowread_thres	numeric value. Cells will be excluded if their total expression level is below this threshold. Default to -Inf.
lowread_high	numeric value. Cells will be excluded if their total expression level is higher than this threshold. Default to Inf.
min_cells	integer value. Genes expressed in less than this value will be excluded.
min_genes	integer value. If a cell has a total number of expressed genes lower than this value, it is excluded.
verbose	a logical indicating whether to print the dataset dimension at each filtering step. Default to TRUE.
data_status	character string. Specifies whether the gene expression levels used for calculation are raw ("Raw"), normalized ("Normalized") or have been imputed ("Smoothed"). Default to "Raw".

juliendelile/Antler documentation built on June 19, 2021, 9 a.m.