A pooled CV is calculated for each biomolecule.
cv_filter(omicsData, use_groups = TRUE)an object of class 'pepData', 'proData', 'metabData',
'lipidData', or 'nmrData' created by as.pepData,
as.proData, as.metabData,
as.lipidData, or as.nmrData, respectively. Note,
if group_designation has not been run, the CV is calculated
based on all samples for each biomolecule.
logical indicator for whether to utilize group information
from group_designation when calculating the CV. Defaults to
TRUE. If use_groups is set to TRUE but group_designation has
not been run on the omicsData object, use_groups will be treated as FALSE.
An S3 object of class 'cvFilt' giving the pooled CV for each biomolecule and additional information used for plotting a data.frame with a column giving the biomolecule name and a column giving the pooled CV value.
For each biomolecule, the CV of each group is calculated as the standard deviation divided by the mean, excluding missing values. A pooled CV estimate is then calculated based on the methods of Ahmed (1995). Any groups consisting of a single sample are excluded from the CV calculation, and thus, from the cv_filter result. If group_designation has not been run on the omicsData object, all samples are considered to belong to the same group.
Ahmed, S.E. (1995). A pooling methodology for coefficient of variation. The Indian Journal of Statistics. 57: 57-75.
library(pmartRdata)
mypep <- group_designation(omicsData = pep_object,
main_effects = "Phenotype")
to_filter <- cv_filter(omicsData = mypep, use_groups = TRUE)
summary(to_filter, cv_threshold = 30)