从R中的频率矩阵创建一个基因类R

Question

我尝试使用“freq2genet”方法在R中创建一个包含“adegenet”的“genet”类。但是一旦我用存储基因频率的数据集调用该方法，就会发生“类型”（字符）参数不正确的错误。在我使用“as.data.frame”之后它仍然会出现。

我该如何解决这个问题？

Answer 1

传递给freq2genet的对象应该是data.frame，其中行是观察值（总体），列是等位基因频率。这是来自ade4:::chevaine示例的数据结构。无论与此有什么不同，都可能是您错误的原因。

> head(chevaine$tab) 
    PGM-2*.090 PGM-2*.098 PGM-2*.100 IDHP-1*.100 IDHP-1*.145 EST-2*.098 EST-2*.100 G3PDH*.085 G3PDH*.100 
P01  0.017  0.150  0.833  1.000  0.000  0.300  0.700  0.217  0.783 
P02  0.083  0.216  0.701  1.000  0.000  0.300  0.700  0.167  0.833 
P03  0.107  0.179  0.714  0.982  0.018  0.250  0.750  0.179  0.821 
P04  0.067  0.200  0.733  1.000  0.000  0.467  0.533  0.217  0.783 
P05  0.103  0.190  0.707  1.000  0.000  0.362  0.638  0.103  0.897 
P06  0.179  0.125  0.696  0.981  0.019  0.250  0.750  0.154  0.846 

> str(freq2genet(chevaine$tab)) 
List of 8 
$ tab  :'data.frame': 27 obs. of 9 variables: 
    ..$ L1.1: num [1:27] 0.3 0.3 0.25 0.467 0.362 0.25 0.217 0.308 0.25 0.31 ... 
    ..$ L1.2: num [1:27] 0.7 0.7 0.75 0.533 0.638 0.75 0.783 0.692 0.75 0.69 ... 
    ..$ L2.1: num [1:27] 0.217 0.167 0.179 0.217 0.103 0.154 0.1 0.038 0.05 0.119 ... 
    ..$ L2.2: num [1:27] 0.783 0.833 0.821 0.783 0.897 0.846 0.9 0.962 0.95 0.881 ... 
    ..$ L3.1: num [1:27] 1 1 0.982 1 1 0.981 0.983 1 0.975 0.976 ... 
    ..$ L3.2: num [1:27] 0 0 0.018 0 0 0.019 0.017 0 0.025 0.024 ... 
    ..$ L4.1: num [1:27] 0.017 0.083 0.107 0.067 0.103 0.179 0.216 0.25 0.175 0.282 ... 
    ..$ L4.2: num [1:27] 0.15 0.216 0.179 0.2 0.19 0.125 0.2 0.115 0.05 0 ... 
    ..$ L4.3: num [1:27] 0.833 0.701 0.714 0.733 0.707 0.696 0.584 0.635 0.775 0.718 ... 
$ center : Named num [1:9] 0.322 0.678 0.114 0.886 0.901 ... 
    ..- attr(*, "names")= chr [1:9] "L1.1" "L1.2" "L2.1" "L2.2" ... 
$ pop.names : Named chr [1:27] "P01" "P02" "P03" "P04" ... 
    ..- attr(*, "names")= chr [1:27] "P01" "P02" "P03" "P04" ... 
$ all.names : Named chr [1:9] "EST-2*.098" "EST-2*.100" "G3PDH*.085" "G3PDH*.100" ... 
    ..- attr(*, "names")= chr [1:9] "L1.1" "L1.2" "L2.1" "L2.2" ... 
$ loc.blocks: Named num [1:4] 2 2 2 3 
    ..- attr(*, "names")= chr [1:4] "L1" "L2" "L3" "L4" 
$ loc.fac : Factor w/ 4 levels "EST-2*","G3PDH*",..: 1 1 2 2 3 3 4 4 4 
$ loc.names : Named chr [1:4] "EST-2*" "G3PDH*" "IDHP-1*" "PGM-2*" 
    ..- attr(*, "names")= chr [1:4] "L1" "L2" "L3" "L4" 
$ all.pop :'data.frame': 9 obs. of 27 variables: 
    ..$ P01: num [1:9] 0.3 0.7 0.217 0.783 1 0 0.017 0.15 0.833 
    ..$ P02: num [1:9] 0.3 0.7 0.167 0.833 1 0 0.083 0.216 0.701 
    ..$ P03: num [1:9] 0.25 0.75 0.179 0.821 0.982 0.018 0.107 0.179 0.714 
    ..$ P04: num [1:9] 0.467 0.533 0.217 0.783 1 0 0.067 0.2 0.733 
    ..$ P05: num [1:9] 0.362 0.638 0.103 0.897 1 0 0.103 0.19 0.707 
    ..$ P06: num [1:9] 0.25 0.75 0.154 0.846 0.981 0.019 0.179 0.125 0.696 
    ..$ P07: num [1:9] 0.217 0.783 0.1 0.9 0.983 0.017 0.216 0.2 0.584 
    ..$ P08: num [1:9] 0.308 0.692 0.038 0.962 1 0 0.25 0.115 0.635 
    ..$ P09: num [1:9] 0.25 0.75 0.05 0.95 0.975 0.025 0.175 0.05 0.775 
    ..$ P10: num [1:9] 0.31 0.69 0.119 0.881 0.976 0.024 0.282 0 0.718 
    ..$ P11: num [1:9] 0.308 0.692 0.154 0.846 0.962 0.038 0.154 0.038 0.808 
    ..$ P12: num [1:9] 0.354 0.646 0.104 0.896 0.979 0.021 0.125 0.104 0.771 
    ..$ P13: num [1:9] 0.317 0.683 0.167 0.833 0.8 0.2 0.033 0.716 0.251 
    ..$ P14: num [1:9] 0.3 0.7 0.083 0.917 0.75 0.25 0.033 0.6 0.367 
    ..$ P15: num [1:9] 0.46 0.54 0.14 0.86 0.74 0.26 0.04 0.62 0.34 
    ..$ P16: num [1:9] 0.369 0.631 0.119 0.881 0.69 0.31 0 0.69 0.31 
    ..$ P17: num [1:9] 0.494 0.506 0.104 0.896 0.747 0.253 0.003 0.659 0.338 
    ..$ P18: num [1:9] 0.321 0.679 0.036 0.964 0.589 0.411 0 0.536 0.464 
    ..$ P19: num [1:9] 0.286 0.714 0.086 0.914 0.871 0.129 0.129 0.343 0.528 
    ..$ P20: num [1:9] 0.267 0.733 0.05 0.95 0.95 0.05 0.15 0.133 0.717 
    ..$ P21: num [1:9] 0.241 0.759 0.121 0.879 0.966 0.034 0.138 0.103 0.759 
    ..$ P22: num [1:9] 0.25 0.75 0.162 0.838 0.941 0.059 0.176 0.059 0.765 
    ..$ P23: num [1:9] 0.339 0.661 0.054 0.946 0.893 0.107 0.125 0.089 0.786 
    ..$ P24: num [1:9] 0.386 0.614 0.068 0.932 0.886 0.114 0.114 0.136 0.75 
    ..$ P25: num [1:9] 0.308 0.692 0.115 0.885 0.823 0.177 0.135 0.01 0.855 
    ..$ P26: num [1:9] 0.338 0.662 0.103 0.897 0.912 0.088 0.088 0.103 0.809 
    ..$ P27: num [1:9] 0.353 0.647 0.074 0.926 0.941 0.059 0.059 0.118 0.823 
- attr(*, "class")= chr [1:2] "genet" "list"