R/combine_techreps.R
combine_techreps.RdFor each biomolecule, this function aggregates the technical replicates of the biological samples using a specified aggregation method
combine_techreps(omicsData, combine_fn = NULL, bio_sample_names = NULL)an object of the class 'lipidData', 'metabData', 'pepData',
'proData', 'nmrData', or 'seqData', created by
as.lipidData, as.metabData,
as.pepData, as.proData,
as.nmrData, or as.seqData, respectively. The
parameter techrep_cnames must have been specified when creating this
object.
a character string specifying the function used to aggregate across technical replicates. Currently supported functions are 'sum' and 'mean'. Defaults to 'sum' for seqData and 'mean' for all other omicsData.
a character string specifying the column in
f_data which contains names by which to label aggregated samples in
omicsData$e_data and omicsData$f_data OR a character vector
with number of elements equal to the number of biological samples. If a
column name is specified, it should have a one-to-one correspondence with
the technical replicate ID column in f_data. Defaults to NULL, in
which case default names are used according to the technical replicate ID
column, which was specified at data object creation.
An object with the same class as omicsData that has been aggregated to the biological sample level
Loss of information after aggregation
| f_data: | If there are columns in f_data that have more than 1 value per biological sample, then for each biological sample, only the first value in that column will be retained. Technical replicate specific information will be lost. |
| group information: | If a grouping structure has been set
using a main effect from f_data that has more than 1 level within any given
biological sample, that grouping structure will be removed. Call
group_designation again on the aggregated data to assign a grouping
structure. |
| sample names: | Identifiers for each biological sample
will replace the identifiers for technical replicates as column names in
e_data as well as the identifier column attr(omicsData,
'fdata_cname') in f_data. |
library(pmartRdata)
pep_object_averaged <- combine_techreps(omicsData = pep_techrep_object)