Package index • iscream

Read data from BED files

General BED files

tabix(): Query lines from a tabixed BED file

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 a matrix from a numeric column of any BED file

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

get_log_level(): Get the current log level

set_log_level(): Set logging level

htslib

htslib_version(): Get htslib version and available features