Create BSSeq object from methylation tabix file

Usage

methy_to_bsseq(methy, out_folder = tempdir(), verbose = TRUE)

Arguments

methy: the NanoMethResult object or path to the methylation tabix file.
out_folder: the folder to store intermediate files. One file is created for each sample and contains columns "chr", "pos", "total" and "methylated".
verbose: TRUE if progress messages are to be printed

Value

a BSSeq object.

Examples

nmr <- load_example_nanomethresult()
bsseq <- methy_to_bsseq(nmr)
#> [2024-08-22 04:05:38] creating intermediate files...
#> [2024-08-22 04:05:38] parsing chr11...
#> [2024-08-22 04:05:38] parsing chr12...
#> [2024-08-22 04:05:38] parsing chr18...
#> [2024-08-22 04:05:38] parsing chr5...
#> [2024-08-22 04:05:38] parsing chr7...
#> [2024-08-22 04:05:38] parsing chrX...
#> [2024-08-22 04:05:38] samples found: B6Cast_Prom_3_cast B6Cast_Prom_3_bl6 B6Cast_Prom_2_cast B6Cast_Prom_2_bl6 B6Cast_Prom_1_cast B6Cast_Prom_1_bl6 
#> [2024-08-22 04:05:38] creating bsseq object...
#> [2024-08-22 04:05:38] reading in parsed data...
#> [2024-08-22 04:05:38] constructing matrices...
#> [2024-08-22 04:05:38] done