run_group_meancor {pmartR}

Calculate the Mean Correlation of a Sample with Respect to Group

Description

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

Usage

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.

Details

Correlation calculations use only complete pairwise observations.

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

Author(s)

Lisa Bramer