calcSegtypeInfo: Build a list of segregation types

Description Usage Arguments Details Value Examples

View source: R/exported_functions.R

Description

For each possible segregation type in an F1 progeny with given parental ploidy (and ploidy2, if parent2 has a different ploidy than parent1) information is given on the segregation ratios, parental dosages and whether the segregation is expected under polysomic, disomic and/or mixed inheritance.

Usage

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calcSegtypeInfo(ploidy, ploidy2=NULL)

Arguments

ploidy

The ploidy of parent 1 (must be even, 2 (diploid) or larger).

ploidy2

The ploidy of parent 2. If omitted (default=NULL) it is assumed to be equal to ploidy.

Details

The names of the segregation types consist of a short sequence of digits (and sometimes letters), an underscore and a final number. This is interpreted as follows, for example segtype 121_0: 121 means that there are three consecutive dosages in the F1 population with frequency ratios 1:2:1, and the 0 after the underscore means that the lowest of these dosages is nulliplex. So 121_0 means a segregation of 1 nulliplex : 2 simplex : 1 duplex. A monomorphic F1 (one single dosage) is indicated as e.g. 1_4 (only one dosage, the 4 after the underscore means that this is monomorphic quadruplex). If UPPERCASE letters occur in the first part of the name these are interpreted as additional digits with values of A=10 to Z=35, e.g. 18I81_0 means a segregation of 1:8:18:8:1 (using the I as 18), with the lowest dosage being nulliplex.
With higher ploidy levels higher numbers (above 35) may be required. In that case each unique ratio number above 35 is assigned a lowercase letter. E.g. one segregation type in octaploids is 9bcb9_2: a 9:48:82:48:9 segregation where the lowest dosage is duplex.
Segregation types with more than 5 dosage classes are considered "complex" and get codes like c7e_1 (again in octoploids): this means a complex type (the first c) with 7 dosage classes; the e means that this is the fifth type with 7 classes. Again the _1 means that the lowest dosage is simplex. It is always possible (and for all segtype names with lowercase letters it is necessary) to look up the actual segregation ratios in the intratio item of the segtype. For octoploid segtype c7e_1 this shows 0:1:18:69:104:69:18:1:0 (the two 0's mean that nulli- and octoplexes do not occur).

Value

A list with for each different segregation type (segtype) one item. The names of the items are the names of the segtypes. Each item is itself a list with components:

Examples

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si4 <- calcSegtypeInfo(ploidy=4) # two 4x parents: a 4x F1 progeny
print(si4[["11_0"]])

si3 <- calcSegtypeInfo(ploidy=4, ploidy2=2) # a 4x and a diplo parent: a 3x progeny
print(si3[["11_0"]])

mdavy86/polymapR documentation built on May 25, 2019, 9:35 p.m.