heapget

Subsections

`heapget`

Return a list of maps of the heap.

Synopsis :

The CarthaGene heapget command is invoked as either one of :

heapget Options
heapget UnitFlag NbMap

Description :

heapget to dump maps from the heap to a list. This command is available for programming...

Arguments :

Options : -u to obtain the synopsys of the normal use, -h to print a one line description, -H to print a short help.
UnitFlag : 'k' for Kosambi, 'h' for Haldane. This field is mandatory, but not used for RH data sets. NbMap : The number of best map to get. If set to 0, all the map of the heap are returned. A positive integer is expected.

Returns :

A list of lists is returned :

{  
   {MapId_0 MapScore_0 {DataSetId_0 OrderScore_0_0 MrkName_0_0_0 CumulDist_0_0_0 MrkName_0_0_1 CumulDist_0_0_1 ... MrkName_0_0_n CumulDist_0_0_n}
                       {DataSetId_1 OrderScore_0_1 MrkName_0_1_0 CumulDist_0_1_0 MrkName_0_1_1 CumulDist_0_1_1 ... MrkName_0_1_n CumulDist_0_1_n'}
                       ...
                       {DataSetId_m OrderScore_0_m MrkName_0_m_0 CumulDist_0_m_0 MrkName_0_m_1 CumulDist_0_m_1 ... MrkName_0_m_n CumulDist_0_m_n''}
   }
   {MapId_1 MapScore_1 {DataSetId_0 OrderScore_1_0 MrkName_1_0_0 CumulDist_1_0_0 MrkName_1_0_1 CumulDist_1_0_1 ... MrkName_1_0_n CumulDist_1_0_n}
                       {DataSetId_1 OrderScore_1_1 MrkName_1_1_0 CumulDist_1_1_0 MrkName_1_1_1 CumulDist_1_1_1 ... MrkName_1_1_n CumulDist_1_1_n'}
                       ...
                       {DataSetId_m OrderScore_1_m MrkName_1_m_0 CumulDist_1_m_0 MrkName_1_m_1 CumulDist_1_m_1 ... MrkName_1_m_n CumulDist_1_m_n''}
   }
   ...
   {MapId_l MapScore_l {DataSetId_0 OrderScore_l_0 MrkName_l_0_0 CumulDist_l_0_0 MrkName_l_0_1 CumulDist_l_0_1 ... MrkName_l_0_n CumulDist_l_0_n}
                       {DataSetId_1 OrderScore_l_1 MrkName_l_1_0 CumulDist_l_1_0 MrkName_l_1_1 CumulDist_l_1_1 ... MrkName_l_1_n CumulDist_l_1_n'}
                       ...
                       {DataSetId_m OrderScore_l_m MrkName_l_m_0 CumulDist_l_m_0 MrkName_l_m_1 CumulDist_l_m_1 ... MrkName_l_m_n CumulDist_l_m_n''}
   }
}

Where l is NbMap, the number of map you get. Where m is the number of "merged by order" data sets. Where n is the number or markers of the map known by the data set.

Example :

# starting with a heap of size 7
CG> heapsize 7

# filling it
CG> dsload Data/bc1.cg
{1 f2 backcross 17 208 /homes/thomas/carthagene/test/Data/bc1.cg}
CG> sem

Map -1 : log10-likelihood =  -485.24
-------:
 Set : Marker List ...
   1 : MS4 MS5 MS13 MS6 MS11 MS17 MS16 MS8 MS7 MS2 MS3 MS9 MS15 MS12 MS20 M...

CG> flips 3 3.0 1
...
CG> heaprint

Map  0 : log10-likelihood =  -454.74
-------:
 Set : Marker List ...
   1 : MS6 MS5 MS4 MS11 MS13 MS16 MS17 MS8 MS7 MS2 MS3 MS9 MS12 MS15 MS19 M...

Map  2 : log10-likelihood =  -454.58
-------:
 Set : Marker List ...
   1 : MS4 MS5 MS6 MS11 MS13 MS17 MS16 MS8 MS7 MS3 MS2 MS9 MS12 MS15 MS19 M...

Map  6 : log10-likelihood =  -454.09
-------:
 Set : Marker List ...
   1 : MS6 MS5 MS4 MS11 MS13 MS16 MS17 MS8 MS7 MS3 MS2 MS9 MS12 MS15 MS19 M...

Map  1 : log10-likelihood =  -452.77
-------:
 Set : Marker List ...
   1 : MS4 MS5 MS6 MS11 MS13 MS16 MS17 MS8 MS7 MS2 MS3 MS9 MS12 MS15 MS20 M...

Map  4 : log10-likelihood =  -452.11
-------:
 Set : Marker List ...
   1 : MS4 MS5 MS6 MS11 MS13 MS16 MS17 MS8 MS7 MS3 MS2 MS9 MS12 MS15 MS20 M...

Map  5 : log10-likelihood =  -451.97
-------:
 Set : Marker List ...
   1 : MS4 MS5 MS6 MS11 MS13 MS16 MS17 MS8 MS7 MS2 MS3 MS9 MS12 MS15 MS19 M...

Map  3 : log10-likelihood =  -451.32
-------:
 Set : Marker List ...
   1 : MS4 MS5 MS6 MS11 MS13 MS16 MS17 MS8 MS7 MS3 MS2 MS9 MS12 MS15 MS19 M...

# getting the 3 best one.
CG> heapget k 3
{3 -451.32 {1 -451.32 MS4 0.0 MS5 3.0 MS6 6.7 MS11 28.2 MS13 36.2 MS16 48.9 M\
S17 64.7 MS8 105.1 MS7 111.0 MS3 125.2 MS2 125.8 MS9 149.4 MS12 164.7 MS15 16\
8.9 MS19 200.8 MS20 203.6 MS1 393.6}} {5 -451.97 {1 -451.97 MS4 0.0 MS5 3.0 M\
S6 6.7 MS11 28.2 MS13 36.2 MS16 48.9 MS17 64.7 MS8 105.1 MS7 111.0 MS2 125.7 \
MS3 126.3 MS9 149.8 MS12 165.1 MS15 169.2 MS19 200.9 MS20 203.7 MS1 393.8}} {\
4 -452.11 {1 -452.11 MS4 0.0 MS5 3.0 MS6 6.7 MS11 28.2 MS13 36.2 MS16 48.9 MS\
17 64.7 MS8 105.1 MS7 111.0 MS3 125.2 MS2 125.8 MS9 149.4 MS12 164.7 MS15 168\
.9 MS20 202.8 MS19 205.6 MS1 395.6}}
CG>