LFMM

LFMM is used by iKISS for testing correlations between kmers and environmental data.

PARAMS:
   LFMM:
      K : 2
      PHENOTYPE_FILE: "pheno.txt"
      PHENOTYPE_PCA_ANALYSIS : false
      CORRECTION: 'BH'
      ALPHA : 0.05

Parameter	Description
K	Number of latent factors used in LFMM association analyses.
PHENOTYPE_FILE	A phenotype file is mandatory for LFMM analysis. Can include PCA results, climate variables, etc.
PHENOTYPE_PCA_ANALYSIS	If true, iKISS automatically runs PCA using the file provided in PHENOTYPE_FILE. If false, iKISS uses the file directly as ‘phenotype’ for LFMM analysis. Kmers are used as ‘genotype’ data
CORRECTION	kmers outliers are obtained using a correction of BONFERONNI, BH or FDR model
ALPHA	modify the alpha cutoff for outlier detection

Here, a example of a phenotype file with climate variables

accession_id        group   b2.Mean_Diurnal_Range   b3.Isothermality        b4.Temp_Seasonality     b5.Max_Temp_of_Warmest_Month    b6.Min_Temp_of_Coldest_Month    b7.Temp_Annual_Range    b8.Mean_Temp_of
_Wettest_Quarter    b9.Mean_Temp_of_Driest_Quarter  b10.Mean_Temp_of_Warmest_Quarter        b11.Mean_Temp_of_Coldest_Quarter        b12.Annual_Precipitation        b13.Precipitation_of_Wettest_Mo
nth b14.Precipitation_of_Driest_Month       b15.Precipitation_Seasonality   b16.Precipitation_of_Wettest_Quarter    b17.Precipitation_of_Driest_Quarter     b18.Precipitation_of_Warmest_Quarter    b19.Precipitation_of_Coldest_Quarter
Clone12     2       99      68      1230    310     166     144     250     226     258     226     1462    249     3       68      573     17      549     17
Clone14     2       100     68      1235    301     155     146     241     217     248     217     1525    259     3       67      603     18      575     18
Clone16     2       93      65      1389    310     168     142     250     223     258     223     1416    264     0       73      579     8       544     8
Clone20     2       154     55      3955    403     123     280     296     234     315     214     118     62      0       184     107     0       45      0
Clone2      1       152     55      3617    403     128     275     287     242     316     220     173     80      0       167     153     0       18      0
Clone4      1       168     51      5719    414     86      328     315     201     322     181     20      12      0       166     18      0       17      0
Clone8      1       NA      NA      NA      NA      NA      NA      NA      NA      NA      NA      NA      NA      NA      NA      NA      NA      NA      NA