Calculate the Mean Correlation of a Sample with Respect to Group

Source: R/filter_objects.R

This function calculates the mean correlation of a sample with all other samples that have the same group membership

run_group_meancor(omicsData, mintR_groupDF, ignore_singleton_groups = TRUE)

Arguments

omicsData

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

mintR_groupDF

data.frame created by group_designation with columns for sample.id and group.

ignore_singleton_groups

logical indicator of whether to remove singleton groups or not; defaults to TRUE. A singleton group is a group consisting of just a single sample. If TRUE, rmd_filter results are returned only for samples in groups of size greater than 1. This is used when calculating the correlation.

Value

data.frame with two elements: Sample.ID, a character vector giving the sample names; and Mean_Correlation, a numeric vector giving the mean correlation values

Details

Correlation calculations use only complete pairwise observations.

Author

Lisa Bramer