Package index • iscream

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

make_mat_bsseq(): Make M/beta and coverage matrices from WGBS BED files

WGBS BED files

summarize_meth_regions(): Summarize methylation information over genomic regions

make_mat_bsseq(): 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