pre_process_methylation {EnMCB} | R Documentation |
This process is optional for the pipeline. This function pre-process the Beta matrix and transform the Beta value into M value.
pre_process_methylation(met,Mvalue,constant_offset,remove_na,remove_percentage)
met |
methylation matrix for CpGs. Rows are the CpG names, columns are samples. |
Mvalue |
Boolean value, TRUE for the M transformation. |
constant_offset |
the constant offset used in the M transformation formula. |
remove_na |
Boolean value, if TRUE ,CpGs with NA values will be removed. |
remove_percentage |
If precentage of NA value exceed the threshold(percentage), the whole CpG probe will be removed. Otherwise, the NA values are replaced with rowmeans. |
Object of class matrix
.
demo_set<-create_demo() pre_process_methylation(demo_set,Mvalue=FALSE)