import_scExp: Read single-cell matrix(ces) into scExp

In vallotlab/ChromSCape: Analysis of single-cell epigenomics datasets with a Shiny App

Read single-cell matrix(ces) into scExp

Description

Combine one or multiple matrices together to create a sparse matrix and cell annotation data.frame.

Usage

import_scExp(file_paths, remove_pattern = "", temp_path = NULL)

Arguments

file_paths	A character vector of file names towards single cell epigenomic matrices (features x cells) (must be .txt / .tsv)
remove_pattern	A string pattern to remove from the sample names. Can be a regexp.
temp_path	In case matrices are stored in temporary folder, a character vector of path towards temporary files. (NULL)

Value

A list containing:

• datamatrix: a sparseMatrix of features x cells

• annot_raw: an annotation of cells as data.frame

Examples

mat1 = mat2 = create_scDataset_raw()$mat
tmp1 = tempfile(fileext = ".tsv")
tmp2 = tempfile(fileext = ".tsv")
write.table(as.matrix(mat1),file=tmp1,sep = "\t",
row.names = TRUE,col.names = TRUE,quote = FALSE)
write.table(as.matrix(mat2),file=tmp2, sep = "\t",
row.names = TRUE,col.names = TRUE,quote = FALSE)
file_paths = c(tmp1,tmp2)
out = import_scExp(file_paths)

vallotlab/ChromSCape documentation built on Oct. 15, 2023, 1:47 p.m.