find_candidate: Find candidate segments for pCSM segments identification.

In Gavin-Yinld/csmFinder: Find putative cell-subset specific methylation (pCSM) loci in single-cell methylomes or bulk methylomes

Description

Determine the pCSM candidate segments statify depth cuttoff, and for single-cell datasets, candidates are determined as the segments covered by both methylated cell and unmethylated cell. For regular datasets, candidates are determined as the segments with at least one totally methylated read and unmethylated read simultaneous.

Usage

find_candidate(segment,depth=10,thread=1,data_type='regular')

Arguments

segment	matrix with segment information
depth	numeric threshold represents the least number of reads (for regular datasets) or cells (for single-cell datasets) covered the candidate segments
thread	number of threads used to identify candidate pCSM segment
data_type	"regular" and "single-cell" represents regular datasets and single-cell datasets, respectively

Examples

### need to get segment object from former steps
#for bulk methylome
#candidate <- find_candidate(segment,depth=10)
  
#for single-cell methylome
#scCandidate <- find_candidate(scSegment,data_type="single-cell",depth=10)

Gavin-Yinld/csmFinder documentation built on Sept. 16, 2019, 3:31 p.m.