# A complex alteration with 2 subclones (copy numbers 3 and 4).
# 2 regions are generated, one for each subclone at 0.8 intra-tumour proportion.
# Contamination (i.e. the opposite of tumour purity) is set to 0.5.
# Only the 5th element of 'times' is set to 1, meaning that only regions with 2 subclones (5th region type) are included, and once per combination.

cnagen(
	times = c(0,0,0,0, 1, 0),
	copynumbers = list(NULL,list(c(3,4)),NULL),
	weights2 = 0.8,
	purities = 0.5
)

# Possible output regions:
#   start end   proportions copy.numbers homozygosity length main.cn main.cn.prop
# 2     1 100 0.5, 0.1, 0.4      2, 3, 4           no    100       4          0.4
# 1   101 200 0.5, 0.4, 0.1      2, 3, 4           no    100       3          0.4


# -------------------
# -------------------

# 3 simple CNA regions of different lengths and copy number 3.

cnagen(
	lengths = list(NULL, c(10,20,50), NULL,NULL,NULL,NULL),
	times = c(0, 1, 0,0,0,0),
	copynumbers = list(list(c(3)),NULL,NULL),
	purities = 1
)

# Possible output regions:
  # start end proportions copy.numbers homozygosity length main.cn main.cn.prop
# 2     1  20        0, 1         2, 3           no     20       3            1
# 3    21  70        0, 1         2, 3           no     50       3            1
# 1    71  80        0, 1         2, 3           no     10       3            1


# -------------------
# -------------------

# 2 normal diploid region of 50 and 100 SNPs and 2 somatic LOH regions (copy numbers 1 and 3) of 10 SNPs repeated twice each.

cnagen(
  lengths = list(c(50,100), NULL, c(10), NULL,NULL,NULL),
  times = c(1, 0, 2, 0,0,0),
  copynumbers = list(list(c(1),c(3)),NULL,NULL),
  purities = 0.2
)

# Possible output regions:
   # start  end proportions copy.numbers homozygosity length main.cn main.cn.prop
 # 1     1   50           1            2           no     50       2          1.0
 # 3    51   60    0.8, 0.2         2, 3      somatic     10       3          0.2
 # 2    61   70    0.8, 0.2         2, 1      somatic     10       1          0.2
 # 5    71   80    0.8, 0.2         2, 3      somatic     10       3          0.2
 # 4    81   90    0.8, 0.2         2, 1      somatic     10       1          0.2
 # 6    91  190           1            2           no    100       2          1.0