write_bedgraphs {methrix} | R Documentation |
Writes bedGraphs from methrix object
write_bedgraphs( m, output_dir = NULL, rm_NA = TRUE, force = FALSE, n_thr = 4, compress = TRUE, SeqStyle = "UCSC", multiBed = NULL, metilene = FALSE, phenoCol = NULL )
m |
|
output_dir |
Output directory name where the files should be saved.
If |
rm_NA |
remove NAs |
force |
forces to create files if they are existing |
n_thr |
Default 4. |
compress |
Whether to compress the output. Default TRUE |
SeqStyle |
Default 'UCSC' with 'chr' prefix. |
multiBed |
Default NULL. If provided a filename, a single bedGraph file with all samples included is generated. |
metilene |
Default FALSE. If TRUE outputs bedgraphs in 'metilene' format that can be directly used for DMR calling with 'metilene'. This option works only when |
phenoCol |
Default NULL. 'condition' column from colData. Only applicable if |
writes bedgraph files to output
data('methrix_data') write_bedgraphs(m = methrix_data, output_dir = './temp') #Export to metline format for DMR calling with metline write_bedgraphs(m = methrix_data, output_dir = "./temp", rm_NA = FALSE, metilene = TRUE,multiBed = "metline_ip", phenoCol = "Condition")