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Read data from BED files

General BED files

tabix() tabix_gr() tabix_raw()
Query records from tabixed BED files
query_chroms()
Query the chromosomes or seqnames from a vector of BED files
summarize_regions()
Summarize information over genomic regions from any BED file
make_mat() make_mat_se() make_mat_gr()
Make a matrix from a numeric column of BED files

WGBS BED files

summarize_meth_regions()
Summarize CpGs methylation information over genomic regions
make_bsseq_mat()
Make M/beta and coverage matrices from WGBS BED files

Utilities

get_granges_string()
GRanges to region strings
get_df_string()
DataFrame to region strings

Multithreading

get_threads()
Get the number of available threads
set_threads()
Set the number of available threads

Logging

set_log_level() get_log_level()
Set and get logging level

htslib

htslib_version()
Get htslib version and available features