Convert map file

Prepare map files for PennCNV and Plink with Default and Target assembly. Four columns in fixed order are required for both default and target map file, they are Chr, Name, Morgan, Position

convert_map(
  default_map,
  target_map,
  chr_set = 29,
  defMap_title = "Default",
  tarMap_title = "Target",
  species = "Bovine",
  col_1 = "green4",
  col_2 = "red1",
  col_3 = "deeppink2",
  col_4 = "deeppink2",
  col_5 = "turquoise3",
  col_6 = "turquoise3",
  legend_position = c(0.9, 0.9),
  height_c = 16,
  width_c = 22,
  height_d = 15,
  width_d = 25
)

Arguments

default_map

the map file to be converted
target_map

the map file used to convert
chr_set

set the number of autosomes
defMap_title

customize the title of default map in plot
tarMap_title

customize the title of target map in plot
species

the name of species
col_1

set color for the type of Match in SNP comparison plot
col_2

set color for the type of Mismatch in SNP comparison plot
col_3

set color for the bar of Target_Map in SNP density plot
col_4

set color for line of Target_map in density plot
col_5

set color for point of Default_Map in SNP density plot
col_6

set color for line of Default_map in SNP density plot
legend_position

default value = c(0.9, 0.9), used to adjust the legend in map comparison plot
height_c

set height for Comparison plot
width_c

set width for comparison plot
height_d

set height for SNP density plot
width_d

set width for SNP density plot

Value

Details of comparison results between given map, and standard input map files used in PennCNV and Plink