read_sparse_matrix {ChromSCape} | R Documentation |
Given one or multiple directories, look in each directory for a combination of the following files :
A 'features' file containing unique feature genomic locations -in tab separated format ( *_features.bed / .txt / .tsv / .gz), e.g. chr, start and end
A 'barcodes' file containing unique barcode names ( _barcode.txt / .tsv / .gz)
A 'matrix' A file containing indexes of non zero entries (_matrix.mtx / .gz)
read_sparse_matrix(files_dir_list, ref = c("hg38", "mm10")[1], verbose = TRUE)
files_dir_list |
A named character vector containing the full path towards folders. Each folder should contain only the Feature file, the Barcode file and the Matrix file (see description). |
ref |
Reference genome (used to filter non-canonical chromosomes). |
verbose |
Print ? |
Returns a list containing a datamatrix and cell annotation
## Not run: sample_dirs = c("/path/to/folder1/", "/path/to/folder2/") names(sample_dirs) = c("sample_1", "sample_2") out <- read_sparse_matrix(sample_dirs, ref = "hg38") head(out$datamatrix) head(out$annot_raw) ## End(Not run)