Computes best lag correlation

This function computes correlation based on best picked lags. The lags indicate delayed changes.

corr.bestlag(data, timepoints, max.lag = NULL, C = NULL,
  penalty = "high", iter = 10)

Arguments

data	a matrix or data frame with rows representing genes and columns representing different timepoints. If data is a data frame, the gene names can be specified using the row.names().
timepoints	a vector of time points used in the dataset
max.lag	a integer value of the maximum lags allowed in the dataset, if null, defaults to the floor of the number of timepoints divided by 4
C	a numeric value of C used in computing weighted correlation, if null, a default is computed based on the penalty argument
penalty	a factor with two levels high and low penalty on the weighted correlation
iter	an integer indicating the number of C values to test for low penalty

Value

a list containing weighted correlation and best lags used in each row

Examples

corr.bestlag(array(rnorm(30), c(5, 6)), max.lag = 1,
          timepoints = c(0, 5, 10, 15, 20, 25), C = 10, penalty = "high")
#> $corr
#>             1           2           3           4
#> 2 -0.42000485                                    
#> 3 -0.39753686 -0.63640974                        
#> 4 -0.32406819 -0.45352765  0.66776179            
#> 5 -0.82938601  0.66038159 -0.04060399 -0.07683003
#> 
#> $lags
#> [1] 1 0 0 0 0
#> 
#> $C
#> [1] 10
#> 
corr.bestlag(array(runif(40, 0, 20), c(4, 10)),
          timepoints = c(0, 0.5, 1.5, 3, 6, 12, 18, 26, 39, 50), penalty = "high")
#> $corr
#>             1           2           3
#> 2 -0.70014226                        
#> 3  0.44803649 -0.06757151            
#> 4  0.44937358  0.06441000  0.33544992
#> 
#> $lags
#> [1] 0 1 0 0
#> 
#> $C
#> [1] 145.7281
#> 
corr.bestlag(matrix(data = rexp(n = 40, 2), nrow = 8),
          timepoints = c(0, 5, 15, 20, 40), penalty = "low", iter = 5)
#> $corr
#>            1          2          3          4          5          6          7
#> 2  0.1165434                                                                  
#> 3 -0.6134928  0.6342942                                                       
#> 4  0.2647404  0.1890557 -0.3092350                                            
#> 5  0.4886498  0.5343446 -0.1617593  0.8589109                                 
#> 6 -0.6891120  0.3297292  0.8930882 -0.3590924 -0.3540430                      
#> 7  0.8761933  0.3717267 -0.4380442  0.6462569  0.8149260 -0.7068592           
#> 8  0.6999832 -0.4231984 -0.9586673  0.5263167  0.4358409 -0.9149395  0.6330580
#> 
#> $lags
#> [1]  0 -1 -1  1 -1  0  1 -1
#> 
#> $C
#> [1] 2680.662
#>