Convert BSseq object to log-methylation-ratio matrix

Creates a log-methylation-ratio matrix from a BSseq object that is useful for dimensionality reduction plots.

Usage

bsseq_to_log_methy_ratio(
  bsseq,
  regions = NULL,
  prior_count = 2,
  drop_na = TRUE
)

Arguments

bsseq

the BSseq object.

regions

the regions to calculate log-methylation ratios over. If left NULL, ratios will be calculated per site.

prior_count

the prior count added to avoid taking log of 0.

drop_na

whether to drop rows with all NA values.

Value

a matrix containing log-methylation-ratios.

Examples

nmr <- load_example_nanomethresult()
bsseq <- methy_to_bsseq(nmr)
#> [2024-08-22 04:04:35] creating intermediate files...
#> [2024-08-22 04:04:35] parsing chr11...
#> [2024-08-22 04:04:35] parsing chr12...
#> [2024-08-22 04:04:35] parsing chr18...
#> [2024-08-22 04:04:35] parsing chr5...
#> [2024-08-22 04:04:35] parsing chr7...
#> [2024-08-22 04:04:35] parsing chrX...
#> [2024-08-22 04:04:35] 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 04:04:35] creating bsseq object...
#> [2024-08-22 04:04:35] reading in parsed data...
#> [2024-08-22 04:04:35] constructing matrices...
#> [2024-08-22 04:04:35] done
regions <- exons_to_genes(NanoMethViz::exons(nmr))
log_m_ratio <- bsseq_to_log_methy_ratio(bsseq, regions)