warning_raw_counts_to_sparse_matrix {ChromSCape} | R Documentation |
Warning for raw_counts_to_sparse_matrix
warning_raw_counts_to_sparse_matrix( files_dir_list, file_type = c("scBAM", "scBED", "SparseMatrix"), peak_file = NULL, n_bins = NULL, bin_width = NULL, genebody = NULL, extendPromoter = 2500, verbose = TRUE, ref = "hg38" )
files_dir_list |
A named character vector of directory containing the raw files |
file_type |
Input file(s) type(s) ('scBED','scBAM','SparseMatrix') |
peak_file |
A file containing genomic location of peaks (NULL) |
n_bins |
The number of bins to tile the genome (NULL) |
bin_width |
The size of bins to tile the genome (NULL) |
genebody |
Count on genes (body + promoter) ? (NULL) |
extendPromoter |
If counting on genes, number of base pairs to extend up or downstream of TSS (2500). |
verbose |
Verbose (TRUE) |
ref |
reference genome to use (hg38) |
Error or warnings if the input are not correct