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11 Calculation is done using the cor function of R software (http://www.r-project.org).org
Thus, the cor function from the caret R package [31] was used to calculate correlations between descriptors.
However, because the LDA failed due to high colinearity, we performed Pearson correlations (cor function with "Pearson" option in R) to identify which genes had highly correlated gene expression.
Correlation analyses were performed in R using the "cor" function.
The correlation matrix was calculated based on the Spearman's rho statistic, cor function (method = spearman).
Correlations were performed using the cor function using the Spearman method.
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In EXPath, Pearson's correlation coefficient and Spearman's rank correlation coefficient are applied by using cor functions in R package to identify genes with co-expression patterns.
To investigate differences in branch length, we calculated the cophenetic correlation coefficient (CCC, from the cophenetic.phylo and cor functions implemented in the R stats and ape packages [ 57, 58]), which measures how well a tree fits the data used to create it on a scale of 0 to 1, with 1 indicating a complete fit.
Using the cor-function in R [ 42] the Pearson correlation between allele frequency estimated by sequencing and genotyping was calculated over 361 SNP loci that were polymorphic in the discovery panel genotyping by randomly selecting the major or minor allele.
Coring sites are indicated in Figure 3.
Henry Siegling, Cor. of King & Beaufain Sts.
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