find_connections: Find out which features are correlated within a specified...

In antonvsdata/amp: Smoothing Metabolomics Analyses

Description

A part of the peak clustering algorithm. Iterates over all possible pairs of features and records a connection between them if a) they have a Pearson correlation coefficient higher than corr_thresh and b) their retention time difference is less than rt_window

Usage

find_connections(data, features, corr_thresh = 0.9, rt_window = 1/60,
  name_col, mz_col, rt_col)

Arguments

data	data frame with the abundances of features, with features as columns
features	data frame with feature information, fData(object)
corr_thresh	numeric, the threshold of correlation to use in linking features
rt_window	numeric, the retention time window to use in linking features. NOTE you need to use the same unit as in the retention time column
name_col	character, name of the column in features that contains feature names
mz_col	character, name of the column in features that contains mass-to-charge ratios
rt_col	character, name of the column in features that contains retention times

Value

a data frame of pairs of signals that are linked together

• x & y: indexes and names of the signals

• cor: correlation coefficient

• mz_diff & rt_diff: mass and retention time difference

antonvsdata/amp documentation built on Jan. 8, 2020, 3:15 a.m.