FilterData: FilterData Function loads in data from 10X

In WeiWeiLab/MalignancyFinder: Malignant cells finder

Description

This function allows you to input 10X single-cell RNAseq profile (loading sparse data matrices provided by 10X genomics), and remove some unwanted cells.

Usage

FilterData(
  PathToData = ".",
  FeatureColumn = 2,
  UniqueFeatures = TRUE,
  FeatureSuffixTrim = FALSE,
  MinFeatures = 200,
  MinUMIs = 500
)

Arguments

PathToData	Folder with barcodes.tsv, features.tsv (or genes.tsv), matrix.mtx. Default is the current folder
FeatureColumn	choose the column of genes.tsv or features.tsv for feature identifiers; default is 2
UniqueFeatures	Logical for unique feature identifiers (default TRUE)
FeatureSuffixTrim	Logicalfor removal of trailing "-1" in cell barcodes (default FALSE)
MinFeatures	Threshold to remove those cell barcodes with found features fewer than it (default 200)
MinUMIs	threshold to remove those cell barcodes with found UMIs fewer than it (default 500)

Value

a sparse matrix containing the expression data will be returned.

Examples

# For output from CellRanger < 3.0
FilterData("outs/filtered_gene_bc_matrices_mex/GRCh38/")
# For output from CellRanger >= 3.0
FilterData("outs/filtered_feature_bc_matrix/")

WeiWeiLab/MalignancyFinder documentation built on June 30, 2020, 12:43 a.m.