pmartR (version 2.4.6)

edata_summary: Creates a list of six Data Frames, one for each summarizing metric

Description

This 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.

Usage

edata_summary(omicsData, by = "sample", groupvar = NULL)

Value

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.

Arguments

omicsData

object of the class 'lipidData', 'metabData', 'pepData', 'proData', or 'nmrData' created by as.lipidData, as.metabData, as.pepData, as.proData, as.nmrData, respectively.

by

character string indicating whether summarizing metrics will be applied by 'sample' or by 'molecule'. Defaults to 'sample'.

groupvar

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.

Details

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.

Examples

if (FALSE) { # requireNamespace("pmartRdata", quietly = TRUE)
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)
}