fuzzygenet: Reading a table of genetic data (diploid individuals)

In ade4: Analysis of Ecological Data : Exploratory and Euclidean Methods in Environmental Sciences

Description

Reads data like char2genet without a priori population

Usage

fuzzygenet(X)

Arguments

X	a data frame of strings of characters (individuals in row, locus in variables), the value coded '000000' or two alleles of 6 characters

Details

In entry, a row is an individual, a variable is a locus and a value is a string of characters, for example, 012028 for a heterozygote carying alleles 012 and 028; 020020 for a homozygote carrying two alleles 020 and 000000 for a not classified locus (missing data).

In exit, a fuzzy array with the following encoding for a locus:
0 0 1 ... 0 for a homozygote
0 0.5 0.5 ... 0 for a heterozygote
p1 p2 p3 ... pm for an unknown where (p1 p2 p3 ... pm) is the observed allelic frequencies for all tha available data.

Value

returns a data frame with the 6 following attributs:

col.blocks	a vector containing the number of alleles by locus
all.names	a vector containing the names of alleles
loc.names	a vector containing the names of locus
row.w	a vector containing the uniform weighting of rows
col.freq	a vector containing the global allelic frequencies
col.num	a factor ranking the alleles by locus

Note

In the exit data frame, the alleles are numbered 1, 2, 3, ... by locus and the loci are called L01, L02, L03, ... for the simplification of listing. The original names are kept.

Author(s)

Daniel Chessel

References

~put references to the literature/web site here ~

See Also

char2genet if you have the a priori definition of the groups of individuals (populations). It may be used on the created object dudi.fca

Examples

data(casitas)
casitas[1:5, ]
casitas <- fuzzygenet(casitas)
attributes(casitas)
rm(casitas)

Example output

     Aat    Amy    Es1    Es2   Es10    Hbb   Gpd1   Idh1   Mod1   Mod2    Mpi
1 100100 080080 094094 100100 100100 120120 100100 100100 110110 100100 100100
2 100100 080100 094094 100100 100100 120120 100100 100125 110110 100100 100100
3 100100 080080 094094 100100 100100 120120 100100 100100 110110 100100 100100
4 100100 080080 094094 100100 100100 120120 100100 100125 100100 100100 100100
5 100100 080080 094094 100100 100100 120120 100100 100100 110110 100100 100100
      Np   Pgm1   Pgm2    Sod
1 100100 100100 100100 100100
2 100100 100100 100100 100100
3 100100 100100 100100 100100
4 100100 100100 100100 100100
5 100100 100100 100100 100100
Warning message:
This function is now deprecated. Please use the 'df2genind' function in the 'adegenet' package. 
$names
 [1] "L01.1" "L01.2" "L02.1" "L02.2" "L03.1" "L03.2" "L04.1" "L04.2" "L04.3"
[10] "L05.1" "L05.2" "L06.1" "L06.2" "L07.1" "L07.2" "L07.3" "L08.1" "L08.2"
[19] "L08.3" "L08.4" "L09.1" "L09.2" "L09.3" "L10.1" "L10.2" "L11.1" "L11.2"
[28] "L12.1" "L12.2" "L12.3" "L12.4" "L13.1" "L13.2" "L13.3" "L14.1" "L14.2"
[37] "L15.1" "L15.2"

$row.names
 [1] "1"  "2"  "3"  "4"  "5"  "6"  "7"  "8"  "9"  "10" "11" "12" "13" "14" "15"
[16] "16" "17" "18" "19" "20" "21" "22" "23" "24" "25" "26" "27" "28" "29" "30"
[31] "31" "32" "33" "34" "35" "36" "37" "38" "39" "40" "41" "42" "43" "44" "45"
[46] "46" "47" "48" "49" "50" "51" "52" "53" "54" "55" "56" "57" "58" "59" "60"
[61] "61" "62" "63" "64" "65" "66" "67" "68" "69" "70" "71" "72" "73" "74"

$class
[1] "data.frame"

$col.blocks
L01 L02 L03 L04 L05 L06 L07 L08 L09 L10 L11 L12 L13 L14 L15 
  2   2   2   3   2   2   3   4   3   2   2   4   3   2   2 

$all.names
     L01.1      L01.2      L02.1      L02.2      L03.1      L03.2      L04.1 
 "Aat.080"  "Aat.100"  "Amy.080"  "Amy.100"  "Es1.094"  "Es1.100"  "Es2.095" 
     L04.2      L04.3      L05.1      L05.2      L06.1      L06.2      L07.1 
 "Es2.098"  "Es2.100" "Es10.060" "Es10.100"  "Hbb.110"  "Hbb.120" "Gpd1.095" 
     L07.2      L07.3      L08.1      L08.2      L08.3      L08.4      L09.1 
"Gpd1.100" "Gpd1.105" "Idh1.050" "Idh1.080" "Idh1.100" "Idh1.125" "Mod1.100" 
     L09.2      L09.3      L10.1      L10.2      L11.1      L11.2      L12.1 
"Mod1.110" "Mod1.120" "Mod2.100" "Mod2.120"  "Mpi.100"  "Mpi.120"   "Np.080" 
     L12.2      L12.3      L12.4      L13.1      L13.2      L13.3      L14.1 
  "Np.085"   "Np.090"   "Np.100" "Pgm1.060" "Pgm1.080" "Pgm1.100" "Pgm2.080" 
     L14.2      L15.1      L15.2 
"Pgm2.100"  "Sod.080"  "Sod.100" 

$loc.names
   L01    L02    L03    L04    L05    L06    L07    L08    L09    L10    L11 
 "Aat"  "Amy"  "Es1"  "Es2" "Es10"  "Hbb" "Gpd1" "Idh1" "Mod1" "Mod2"  "Mpi" 
   L12    L13    L14    L15 
  "Np" "Pgm1" "Pgm2"  "Sod" 

$row.w
 [1] 0.01351351 0.01351351 0.01351351 0.01351351 0.01351351 0.01351351
 [7] 0.01351351 0.01351351 0.01351351 0.01351351 0.01351351 0.01351351
[13] 0.01351351 0.01351351 0.01351351 0.01351351 0.01351351 0.01351351
[19] 0.01351351 0.01351351 0.01351351 0.01351351 0.01351351 0.01351351
[25] 0.01351351 0.01351351 0.01351351 0.01351351 0.01351351 0.01351351
[31] 0.01351351 0.01351351 0.01351351 0.01351351 0.01351351 0.01351351
[37] 0.01351351 0.01351351 0.01351351 0.01351351 0.01351351 0.01351351
[43] 0.01351351 0.01351351 0.01351351 0.01351351 0.01351351 0.01351351
[49] 0.01351351 0.01351351 0.01351351 0.01351351 0.01351351 0.01351351
[55] 0.01351351 0.01351351 0.01351351 0.01351351 0.01351351 0.01351351
[61] 0.01351351 0.01351351 0.01351351 0.01351351 0.01351351 0.01351351
[67] 0.01351351 0.01351351 0.01351351 0.01351351 0.01351351 0.01351351
[73] 0.01351351 0.01351351

$col.freq
      L01.1       L01.2       L02.1       L02.2       L03.1       L03.2 
0.148648649 0.851351351 0.750000000 0.250000000 0.702702703 0.297297297 
      L04.1       L04.2       L04.3       L05.1       L05.2       L06.1 
0.081081081 0.195945946 0.722972973 0.116438356 0.883561644 0.465753425 
      L06.2       L07.1       L07.2       L07.3       L08.1       L08.2 
0.534246575 0.375000000 0.534722222 0.090277778 0.101351351 0.006756757 
      L08.3       L08.4       L09.1       L09.2       L09.3       L10.1 
0.608108108 0.283783784 0.128378378 0.797297297 0.074324324 0.689189189 
      L10.2       L11.1       L11.2       L12.1       L12.2       L12.3 
0.310810811 0.794520548 0.205479452 0.061643836 0.089041096 0.061643836 
      L12.4       L13.1       L13.2       L13.3       L14.1       L14.2 
0.787671233 0.027397260 0.130136986 0.842465753 0.082191781 0.917808219 
      L15.1       L15.2 
0.121621622 0.878378378 

$col.num
 L01  L01  L02  L02  L03  L03  L04  L04  L04  L05  L05  L06  L06  L07  L07  L07 
 Aat  Aat  Amy  Amy  Es1  Es1  Es2  Es2  Es2 Es10 Es10  Hbb  Hbb Gpd1 Gpd1 Gpd1 
 L08  L08  L08  L08  L09  L09  L09  L10  L10  L11  L11  L12  L12  L12  L12  L13 
Idh1 Idh1 Idh1 Idh1 Mod1 Mod1 Mod1 Mod2 Mod2  Mpi  Mpi   Np   Np   Np   Np Pgm1 
 L13  L13  L14  L14  L15  L15 
Pgm1 Pgm1 Pgm2 Pgm2  Sod  Sod 
15 Levels: Aat Amy Es1 Es10 Es2 Gpd1 Hbb Idh1 Mod1 Mod2 Mpi Np Pgm1 ... Sod

ade4 documentation built on May 2, 2019, 5:50 p.m.