In this program, you are provided with phenotype pair counts of F2 offspring at two research institutes. The key different between this work and previous work is that now we consider two genes instead of one. The phenotype pairs are the (shape, color) of peas from a pea plant. It turns out that there are two separate genes that code for these phenotypes. We shall call them Shape and Color. Gregor Mendel originally recorded these experiments in green peas. Using the notation: R = Round (dominant) allele at Shape gene; r = Wrinkled (recessive) allele at Shape gene; Y = Yellow (dominant) allele at Color gene; y = Green (recessive) allele at Color gene; then the shape and color of any pea can be determined by studying the genotypes at each gene. It turns out that, when one mates a plant that is homozygous for the dominant alleles (RRYY) with a plant that is homozygous for the recessive alleles (rryy), the F1 generation are heterozygous at both genes, as with a single gene disorder. It is straightforward to see that phenotype pairs in all F1 peas are (Round, Yellow). If we cross two F1 pea plants, then, as documented in the slide presentation, we have the phenotype pair ratios (Round,Yellow):(Round,Green):(Wrinkled,Yellow):(Wrinkled,Green) are 9:3:3:1. In this assignment you are provided with randomly-generated counts of the four phenotype pairs listed above. Your task is two-fold: (1) To perform a chi-square goodness of fit test on the F2 observed data at each research institute and report the ChiSquare statistic and the corresponding p-value, under the specification that the ratio of the four phenotype pairs above are 9:3:3:1. (2) To apply the Fisher Combined P-value Test to the p-values from each research institute and decide whether you reject or do not reject the null hypothesis that the phenotype pair ratios are 9:3:3:1 at each research institute. RESEARCH INSTITUTE 01 F2 DATA Phenotype Pair (Shape,Color) (Round,Yellow) (Round,Green) (Wrinkled,Yellow) (Wrinkled,Green) 28 12 5 7 RESEARCH INSTITUTE 02 F2 DATA Phenotype Pair (Shape,Color) (Round,Yellow) (Round,Green) (Wrinkled,Yellow) (Wrinkled,Green) 31 12 18 5
In this program, you are provided with phenotype pair counts of
F2 offspring at two research institutes. The key different between
this work and previous work is that now we consider two genes instead of one.
The phenotype pairs are the (shape, color) of peas from a pea plant. It turns out
that there are two separate genes that code for these
Shape and Color. Gregor Mendel originally recorded these experiments in
green peas. Using the notation:
R = Round (dominant) allele at Shape gene;
r = Wrinkled (recessive) allele at Shape gene;
Y = Yellow (dominant) allele at Color gene;
y = Green (recessive) allele at Color gene;
then the shape and color of any pea can be determined
by studying the genotypes at each gene.
It turns out that, when one mates a plant that is homozygous for the dominant
alleles (RRYY) with a plant that is homozygous for the recessive alleles (rryy),
the F1 generation are heterozygous at both genes, as with a single gene disorder.
It is straightforward to see that phenotype pairs in all F1 peas are (Round, Yellow).
If we cross two F1 pea plants, then, as documented in the slide presentation, we have
the phenotype pair ratios (Round,Yellow):(Round,Green):(Wrinkled,Yellow):(Wrinkled,Green)
are 9:3:3:1.
In this assignment you are provided with randomly-generated counts
of the four phenotype pairs listed above.
Your task is two-fold:
(1) To perform a chi-square goodness of fit test on the F2 observed data
at each research institute and report the ChiSquare statistic and
the corresponding p-value, under the specification that the ratio of
the four phenotype pairs above are 9:3:3:1.
(2) To apply the Fisher Combined P-value Test to the p-values from each
research institute and decide whether you reject or do not reject
the null hypothesis that the phenotype pair ratios are 9:3:3:1
at each research institute.
RESEARCH INSTITUTE 01
F2 DATA
Phenotype Pair (Shape,Color)
(Round,Yellow) (Round,Green) (Wrinkled,Yellow) (Wrinkled,Green)
28 12 5 7
RESEARCH INSTITUTE 02
F2 DATA
Phenotype Pair (Shape,Color)
(Round,Yellow) (Round,Green) (Wrinkled,Yellow) (Wrinkled,Green)
31 12 18 5
You may make use of the online goodness of fit test calculator for your assignment, as long as you provide the null hypothesis, the statistic value, the degrees of freedom, and the p-value. link to online calculator:
https://www.socscistatistics.com/tests/goodnessoffit/default2.aspx
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