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Fig. 4 | BMC Genomics

Fig. 4

From: GCA: an R package for genetic connectedness analysis using pedigree and genomic data

Fig. 4

A flow diagram of three prediction error correlation (r) statistics. The group average r (r_GrpAve) is shown in A. A1: Prediction error variance (PEV) matrix of seven individuals. A2: Calculate the mean of prediction error variance / covariance within the unit (PEV_mean) and mean of prediction error covariance across the unit (PEC_mean). A3: Group average r is a correlation calculated from PEV_mean and PEC_mean. The calculation of individual average r (r_IdAve) involving seven individuals is displayed in B. B1: Prediction error variance (PEV) matrix of seven individuals. B2: Calculate pairwise correlation coefficients of individuals between units using PEV and prediction error covariance (PEC). Subscripts i and j refer to the ith and jth individuals in units 1 and 2, respectively. B3: Individual average r is calculated as the average of pairwise prediction error correlation coefficients of individuals across units. The r of contrast (r_Contrast) is shown in C. r_Contrast is calculated from the product of the transpose of the contrast vector (x), r matrix, and the contrast vector

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