filter_cirBed: Filter the bed file generated by CircleMap

In huangyizR/test: What the Package Does (One Line, Title Case)

Description

This function performs filtration of the raw bed file generated by CircleMap

Usage

filter_cirBed(cirBed, scores = 50, discord = 4, splitreads = 4, length = 3e+07)

Arguments

cirBed	get by cirBed = read.table("my_unknown_circleMap.bed", sep = tab, stringsAsFactors = FALSE)
scores	Threshold of Circle score. score below would be removed
discord	Threshold of number of discordant read pairs supporting the detected circular DNA. Below the threshold would be reomved
splitreads	Threshold of number of split reads supporting the detected circular DNA. Below the threshold would be removed
length	Maximum length of the circular DNA detected.

Value

a data frame with : c("Chromosome","start_coord", "end_coord", "dis_cord", "split_reads", "circle_score", "Mean_coverage", "SD", "CISC", "CIEC", "coverage_continuity")

huangyizR/test documentation built on June 17, 2020, 12:32 a.m.