Compare CNVR

The idea of CNVRs comparison is to find out how many CNVRs and how many length are overlapped between different CNVR results.

compare_cnvr(
  cnvr_def,
  cnvr_tar,
  def_tar_map = NULL,
  width_1 = 15,
  height_1 = 15,
  hjust_prop = 0,
  hjust_num = 1.5,
  folder = "compare_cnvr",
  col_1 = "gray20",
  col_2 = "springgreen4"
)

Arguments

cnvr_def	'def' is 'default' indicate the first input file, standard input file was generated by 'call_cnvr' function.
cnvr_tar	'tar' is 'target' indicate the second input file, standard input file was generated by 'call_cnvr' function.
def_tar_map	Unused at the moment. map file contains coordinates in both version of map. only need in comparison between the results from different versions. default file is generated from convert_map function
width_1	set the width of final plot size, unit is 'cm'
height_1	set the height of final plot size, unit is 'cm'
hjust_prop	default value is 0.0. used to adjust horizontal position of the number of overlapped CNVR in the plot
hjust_num	default value is 1.5. used to adjust horizontal position of the number of overlapped CNVR in the plot
folder	set name of folder to save results
col_1	set color for overlapped bar
col_2	set color for non-overlapped bar

Value

Details comparison results of CNVRs between input lists

Details

The six standards are defined for CNVR comparison: 1) overlapped 1.same start and end, same SNP inside, fully overlap 2.same start and end, different snp number, fully overlap 3.different start or end, overlapped, partial overlap 2) non-overlap 4.missing start or end position 5.End <= start 6.different start or end, non-overlap according to the condition, the first thing is to match coordinates for both version then find overlap CNVR and non overlap CNVR then summarize how many CNVRs are in above standards