2.1.1 Experiment Table

The experiment table summarizes the parameters of each mapping experiment. This table contains the following fields:

• map (string) : the name of the mapping experiment which must be unique.
• mapping.function (string) : the name of the mapping function used to build the genetic map for this mapping experiment. Presently the possible values are:
  • haldane
  • kosambi
• mapping.unit (string) : the unit of the genetic distances of the genetic linkage map. Possible values are M for Morgan or cM for centiMorgan.
• mapping expansion (boolean) : 1 if the genetic linkage map of this mapping experiment must be rescaled.
• mapping.cross : the cross design used to build the map (may differ from the cross.type).
• cross.type (string) : the cross design used to build the genetic linkage map. MetaQTL is able to deal with various types of experimental designs. The design is encoded by a string of characters. For example BC stands for backcross, SFi stands for selfed intercross lines and the integer i indicates the generation (if i=2 then we have a classical F2). Experimental designs presently supported are listed in the table below (the cross type naming and labelling convention comes from QTLCartographer).

  Cross type	Code	Example
  Backcross	BC	BC
  Selfed generation i intercross	SFi	SF2
  Randomly mated generation i intercross	RFi	RF3
  Recombined Inbred via selfing	RI0	RI0
  Recombined Inbred via sib mating	RI1	RI1
  Intermated (i generations) Recombined Inbred via selfing	IRI0i	IRI04
  Intermated (i generations) Recombined Inbred via sib mating	IRI1i	IRI13

• cross.name (string) : the name of the cross.
• cross.size (integer): the number of individuals used to build the genetic linkage map.

For example, inserting 5 mapping experiments leads to the following file

map mapping.function mapping.unit mapping.expansion cross.type cross.name cross.size exp1 haldane cM 0 SF2 Mo17xB73 200 exp2 haldane cM 1 RF4 F2xF252 300 exp3 kosambi M 0 BC H99xF2 150 exp4 haldane cM 1 IRI04 F2xF252 400 exp5 haldane cM 0 SF4 Mo17xF2 150