uniqueness_gtest: Determine Unique and Common Masses Between Two Groups

In EMSL-Computing/fticRanalysis: Analysis and visualization tools for FT-MS data

Determine Unique and Common Masses Between Two Groups

Description

Use a g-test to compare two groups and determine which peaks are uniquely expressed in each group based on a p-value threshold

Usage

uniqueness_gtest(
  edata_df,
  group_df,
  data_scale,
  pres_fn,
  pres_thresh,
  pvalue_thresh = 0.05
)

Arguments

edata_df	data.frame giving samples expression profiles for samples belonging to one of two groups
group_df	data.frame giving sample names and column indicating group membership. Column indicating group membership should be named 'Group' and have exactly two unique values
data_scale	character string giving scale the data is on. Current acceptable values are: "log", "log2", "log10", "abundance", "pres"
pres_fn	character string indicating the function to use when determining if a peak/compound is present for a group. Current options include "nsamps" and "prop".
pres_thresh	numeric value indicating the threshold (e.g. number of samples, proportion of samples, etc.), inclusive, that are required for a peak to be considered present/observed in a group.
pvalue_thresh	p-value threshold at which masses with a g-test p-value less than or equal to pval_threshold are considered to be unique to the group with more observed proportion/number of samples, which also exceeds pres_thresh

Author(s)

Lisa Bramer

EMSL-Computing/fticRanalysis documentation built on Dec. 18, 2024, 9:51 p.m.