age.apply: Age Category Specific apply Function
In myTAI: Evolutionary Transcriptomics

Description Usage Arguments Details Value Author(s) See Also Examples

This function performs the split-apply-combine methodology on Phylostrata or Divergence Strata stored within the input ExpressionSet.

This function is very useful to perform any phylostratum or divergence-stratum specific analysis.

1	age.apply(ExpressionSet, FUN, ..., as.list = FALSE)

`ExpressionSet`	a standard PhyloExpressionSet or DivergenceExpressionSet object.
`FUN`	a function to be performed on the corresponding expression matrix of each phylostratum or divergence-stratum.
`...`	additional arguments of FUN.
`as.list`	a boolean value specifying whether the output format shall be a matrix or a list object.

This function uses the split function to subset the expression matrix into phylostratum specific sub-matrices. Internally using lapply, any function can be performed to the sub-matrices. The return value of this function is a numeric matrix storing the return values by FUN for each phylostratum and each developmental stage s. Note that the input FUN must be an function that can be applied to a matrix (e.g., colMeans or RE). In case you use an an anymous function you coud use function(x) apply(x , 2 , var) as an example to compute the variance of each phylostratum and each developmental stage s.

Either a numeric matrix storing the return values of the applied function for each age class or a numeric list storing the return values of the applied function for each age class in a list.

Hajk-Georg Drost

split, tapply, lapply, RE, REMatrix

 
 # source the example dataset
 data(PhyloExpressionSetExample)
 
# Example 1
# get the relative expression profiles for each phylostratum
age.apply(PhyloExpressionSetExample, RE)

# this is analogous to 
REMatrix(PhyloExpressionSetExample)
# Example 2
# compute the mean expression profiles for each phylostratum
age.apply(PhyloExpressionSetExample, colMeans)

# Example 3
# compute the variance profiles for each phylostratum
age.apply(PhyloExpressionSetExample, function(x) apply(x , 2 , var))

# Example 4
# compute the range for each phylostratum
# Note: in this case, the range() function returns 2 values for each phylostratum
# and each developmental stage, hence one should use the argument 'as.list = TRUE'
# to make sure that the results are returned properly 
age.apply(PhyloExpressionSetExample, function(x) apply(x , 2 , range), as.list = TRUE)