R/edata_summary.R
edata_summary.RdThis function takes in an omicsData object and returns a summary of the e_data component. The six summarizing metrics include the mean, standard deviation, median, percent observed, minimum, and maximum.
edata_summary(omicsData, by = "sample", groupvar = NULL)object of the class 'lipidData', 'metabData', 'pepData',
'proData', or 'nmrData' created by as.lipidData,
as.metabData, as.pepData,
as.proData, as.nmrData, respectively.
character string indicating whether summarizing metrics will be applied by 'sample' or by 'molecule'. Defaults to 'sample'.
a character vector with no more than two variable names that
should be used to determine group membership of samples. The variable name
must match a column name from f_data. Defaults to NULL, in which
case group_DF attribute will be used.
A list of six data frames, of class 'dataRes' (data Result), which are the results of applying the metrics (mean, standard deviation, median, percent observed, minimum and maximum) to omicsData$e_data.
If groupvar is NULL and group_designation has not been applied to
omicsData, then the metrics will be applied to each column of e_data (when
by = 'sample) or to each row of e_data (when by = 'molecule'). When
groupvar is provided, it must match a column name from f_data, this
column of f_data is used to group e_data in order to apply the metrics.
library(pmartRdata)
mylipid <- edata_transform(omicsData = lipid_pos_object, data_scale = "log2")
mylipid <- group_designation(omicsData = mylipid, main_effects = "Virus")
result <- edata_summary(omicsData = mylipid, by = "sample", groupvar = NULL)