splitDataByBed | R Documentation |
This function splits the methylation data into regions based on the genomic annotation provided under the form of a 1-based BED file
splitDataByBed( dat, chr, bed, gap = -1, min.cpgs = 50, max.cpgs = 2000, verbose = TRUE )
dat |
a data frame with rows as individual CpGs appearing
in all the samples. The first 4 columns should contain the information of
|
chr |
character vector containing the chromosome information. Its length
should be equal to the number of rows in |
bed |
character, path to the 1-based BED file containing the annotations |
gap |
integer defining the maximum gap that is allowed between
two regions to be considered as overlapping.
According to the |
min.cpgs |
positive integer defining the minimum number of CpGs within a region for the algorithm to perform optimally. The default value is 50. |
max.cpgs |
positive integer defining the maximum number of CpGs within a region for the algorithm to perform optimally. The default value is 2000. |
verbose |
logical indicates if the algorithm should provide progress report information. The default value is TRUE. |
A named list
of data.frame
containing the data of each
independent region.
Audrey Lemaçon
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