pre_filter: Filter Data

In kgellatl/SignallingSingleCell: Network Analysis for single cell RNA sequencing Data (sc-RNASeq)

Description

This function will filter the data to remove cells and/or genes

Usage

pre_filter(
  input,
  minUMI = 0,
  maxUMI = NA,
  threshold = NA,
  minCells = NA,
  print_progress = TRUE
)

Arguments

input	the input ex_sc
minUMI	min number of UMIs per cell
maxUMI	max number of UMIs per cell
threshold	UMI threshold for gene detection
minCells	number of cells expressed above threshold for a given gene
print_progress	will print progress if TRUE

Details

When processing the data, low quality cells may contain very few UMIs, while some overrepresented cell barcodes may indicate barcode bleedover or cell doublets. Filtering out both low and high UMI count cells is recommended before normalization.

Examples

filtered_data <- filter_UMIs(input = ex_sc_example, minUMI = 1000, maxUMI = 10000, threshold = 1, minCells = 10, print_progress = TRUE)

kgellatl/SignallingSingleCell documentation built on Dec. 29, 2021, 4:12 p.m.